Simulations

Simulations of relevance to SARS-CoV-2
Data classification:
  • Simulations: The datasets produced as a result of applying the models to different scientific techniques.
  • Proteins: The biological proteins associated with the SARS-CoV-2 virus and host.
  • Structures: Data defining structures determined by experimental methods and referenced via a unique identifier such as a PDB ID.
  • Models: Derived, integrated, or refined structures from multiple data sources prepared for different computational tasks.

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3CLpro ACE2 BoAT1 E protein Fc receptor Furin Helicase IL6R M protein Macrodomain N protein NSP1 NSP10 NSP11 NSP14 NSP15 NSP16 NSP2 NSP4 NSP6 NSP7 NSP8 NSP9 ORF10 ORF3a ORF6 ORF7a ORF7b ORF8 PD-1 PLpro RdRP TMPRSS2 fusion core p38 spike virion

Simulations of Virion Particle

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Simulations of Viral Spike Proteins

Viral Spike Fusion Core


SARS-CoV-2 Spike (S) glycoprotein

Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

Riken CPR TMS, TMD1_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (51 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein, no water or ions (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

SIRAH-CoV2 initiative - S1 Receptor Binding Domain in complex with human antibody CR3022 (12 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycans have been removed from the structures.

The file 6W41_SIRAHcg_rawdata.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W41_SIRAHcg_12us_prot.tar contains only the protein coordinates, while 6W41_SIRAHcg_12us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W41_SIRAHcg_12us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6W41_SIRAHcg_prot.prmtop 6W41_SIRAHcg_prot_12us_skip10ns.ncrst 6W41_SIRAHcg_prot_12us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.6 GB)
Represented Proteins: spike RBD
Represented Structures: 6W41
Models: ---

SIRAH-CoV2 initiative - S2 Spike core fragment in postfusion state (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M1V_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot_10us_skip10ns.ncrst 6M1V_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (17.8 GB)
Represented Proteins: spike S2
Represented Structures: 6M1V
Models: ---

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2

SIRAH-CoV2 initiative - Glycosylated RBD (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike´s RBD glycosylated at Asn331 and Asn343. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI.

There are two different sets of simulations corresponding to Core Complex and High Mannose. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and RBD-Man9_SIRAHcg_rawdata_6-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Analogous information for Core-complex glycosylations is contained in files RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar.

Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in SIRAHcg_10us_prot.tar contains only the protein coordinates, while SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file RBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd RBD-Core-complex_SIRAHcg_prot.prmtop RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.ncrst RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (16.4 GB)
Represented Proteins: spike RBD
Represented Structures: 6VSB
Models: ---

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Riken CPR TMS, TMD3_toDown trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Trajectories of full-length SPIKE protein in the Closed state. (1.7 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Closed state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (13 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Riken CPR TMS, MD2_Down trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

Riken CPR TMS, TMD2_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481 (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of a Spike’s RBD from SARS-CoV2 glycosylated at Asn331, 343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files 6XEY-RBD-3Man9_SIRAHcg_0-4us.tar, 6XEY-RBD-3Man9_SIRAHcg_4-8us.tar, and 6XEY-RBD-3Man9_SIRAHcg_8-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in 6XEY-RBD-3Man9_SIRAHcg_glycoprot_10us.tar contains only the protein coordinates, while 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6XEY-RBD-3Man9_SIRAHcg_glycoprot.prmtop 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.ncrst 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (11.2 GB)
Represented Proteins: spike RBD
Represented Structures: 6XEY
Models: ---

1 microsecond trajecotry of glycosylated spike protein in open state for pdb:6VSB embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in open state (pdb:6VSB) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the open state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

Interaction between the SARS-CoV-2 spike and the αβγδ nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the αβγδ nicotinic acetylcholine receptor from Tetronarce californica (formerly Torpedo californica). ABGD_nAChR-spike.tar.gz contains the following files ABGD_nAChR-spike_complex.pdb ABGD_nAChR-spike_r1.tpr ABGD_nAChR-spike_r1.xtc ABGD_nAChR-spike_r2.tpr ABGD_nAChR-spike_r2.xtc ABGD_nAChR-spike_r3.tpr ABGD_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

ABGD_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/ABGD_nAChR-spike_complex.pdb
Models: ---

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

Trajectories of full-length SPIKE protein in the Open state (N165A / N234A mutations). (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state bearing N165A and N234A mutations, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

Riken CPR TMS, MD1_Down trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

Riken CPR TMS, TMD1_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD2_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD3_toUp trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

Interaction between the SARS-CoV-2 spike and the α4β2 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α4β2 nicotinic acetylcholine receptor. A4B2_nAChR-spike.tar.gz contains the following files. A4B2_nAChR-spike_complex.pdb A4B2_nAChR-spike_r1.tpr A4B2_nAChR-spike_r1.xtc A4B2_nAChR-spike_r2.tpr A4B2_nAChR-spike_r2.xtc A4B2_nAChR-spike_r3.tpr A4B2_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A4B2_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/A4B2_nAChR-spike_complex.pdb
Models: ---

Folding@home simulations of the SARS-CoV-2 spike protein (1.2 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of the SARS-CoV-2 spike protein, simulated using Folding@Home. The dataset comprises 3 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14217) or OpenMM (PROJ14235 and PROJ14561) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14217 and PROJ14253 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14253 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14561 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/spike/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (6.5 TB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: ---

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (67 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

1 microsecond trajecotry of glycosylated spike protein in closed state for pdb:6VXX embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in closed state (pdb:6VXX) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the closed state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Riken CPR TMS, MD2_Up trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

Trajectories of full-length SPIKE protein in the Open state. (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

Interaction between the SARS-CoV-2 spike and the α7 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α7 nicotinic acetylcholine receptor. A7_nAChR-spike.tar.gz contains all the following files. A7_nAChR-spike_complex.pdb A7_nAChR-spike_r1.tpr A7_nAChR-spike_r1.xtc A7_nAChR-spike_r2.tpr A7_nAChR-spike_r2.xtc A7_nAChR-spike_r3.tpr A7_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A7_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub/MulhollandGroup/nAChR-spike_interaction/A7_nAChR-spike_complex.pdb
Models: ---

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (62 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

Riken CPR TMS, MD1_Up trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (166 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model (60 ns )

Dmitry Morozov
University of Jyvaskyla
This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The protein was solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.1Charmm27
Input and Supporting Files:

trimer

Trajectory: Get Trajectory (2.0 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: SARS-CoV-2 spike protein trimer (closed state) model for MD simulations

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulation was conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (49 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Inhibiting cleavage of the SARS-CoV-2 spike protein

Riken CPR TMS, TMD1_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (51 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein, no water or ions (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

SIRAH-CoV2 initiative - S1 Receptor Binding Domain in complex with human antibody CR3022 (12 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycans have been removed from the structures.

The file 6W41_SIRAHcg_rawdata.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W41_SIRAHcg_12us_prot.tar contains only the protein coordinates, while 6W41_SIRAHcg_12us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W41_SIRAHcg_12us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6W41_SIRAHcg_prot.prmtop 6W41_SIRAHcg_prot_12us_skip10ns.ncrst 6W41_SIRAHcg_prot_12us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.6 GB)
Represented Proteins: spike RBD
Represented Structures: 6W41
Models: ---

SIRAH-CoV2 initiative - S2 Spike core fragment in postfusion state (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M1V_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot_10us_skip10ns.ncrst 6M1V_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (17.8 GB)
Represented Proteins: spike S2
Represented Structures: 6M1V
Models: ---

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

SIRAH-CoV2 initiative - Glycosylated RBD (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike´s RBD glycosylated at Asn331 and Asn343. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI.

There are two different sets of simulations corresponding to Core Complex and High Mannose. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and RBD-Man9_SIRAHcg_rawdata_6-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Analogous information for Core-complex glycosylations is contained in files RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar.

Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in SIRAHcg_10us_prot.tar contains only the protein coordinates, while SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file RBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd RBD-Core-complex_SIRAHcg_prot.prmtop RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.ncrst RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (16.4 GB)
Represented Proteins: spike RBD
Represented Structures: 6VSB
Models: ---

Riken CPR TMS, MD2_Down trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

Riken CPR TMS, TMD2_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

Riken CPR TMS, TMD3_toDown trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Trajectories of full-length SPIKE protein in the Closed state. (1.7 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Closed state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (13 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Interaction between the SARS-CoV-2 spike and the αβγδ nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the αβγδ nicotinic acetylcholine receptor from Tetronarce californica (formerly Torpedo californica). ABGD_nAChR-spike.tar.gz contains the following files ABGD_nAChR-spike_complex.pdb ABGD_nAChR-spike_r1.tpr ABGD_nAChR-spike_r1.xtc ABGD_nAChR-spike_r2.tpr ABGD_nAChR-spike_r2.xtc ABGD_nAChR-spike_r3.tpr ABGD_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

ABGD_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/ABGD_nAChR-spike_complex.pdb
Models: ---

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481 (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of a Spike’s RBD from SARS-CoV2 glycosylated at Asn331, 343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files 6XEY-RBD-3Man9_SIRAHcg_0-4us.tar, 6XEY-RBD-3Man9_SIRAHcg_4-8us.tar, and 6XEY-RBD-3Man9_SIRAHcg_8-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in 6XEY-RBD-3Man9_SIRAHcg_glycoprot_10us.tar contains only the protein coordinates, while 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6XEY-RBD-3Man9_SIRAHcg_glycoprot.prmtop 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.ncrst 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (11.2 GB)
Represented Proteins: spike RBD
Represented Structures: 6XEY
Models: ---

1 microsecond trajecotry of glycosylated spike protein in open state for pdb:6VSB embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in open state (pdb:6VSB) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the open state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

Trajectories of full-length SPIKE protein in the Open state (N165A / N234A mutations). (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state bearing N165A and N234A mutations, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

Riken CPR TMS, MD1_Down trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

Interaction between the SARS-CoV-2 spike and the α4β2 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α4β2 nicotinic acetylcholine receptor. A4B2_nAChR-spike.tar.gz contains the following files. A4B2_nAChR-spike_complex.pdb A4B2_nAChR-spike_r1.tpr A4B2_nAChR-spike_r1.xtc A4B2_nAChR-spike_r2.tpr A4B2_nAChR-spike_r2.xtc A4B2_nAChR-spike_r3.tpr A4B2_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A4B2_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/A4B2_nAChR-spike_complex.pdb
Models: ---

Folding@home simulations of the SARS-CoV-2 spike protein (1.2 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of the SARS-CoV-2 spike protein, simulated using Folding@Home. The dataset comprises 3 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14217) or OpenMM (PROJ14235 and PROJ14561) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14217 and PROJ14253 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14253 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14561 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/spike/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (6.5 TB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: ---

Riken CPR TMS, TMD1_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD2_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD3_toUp trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (67 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

1 microsecond trajecotry of glycosylated spike protein in closed state for pdb:6VXX embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in closed state (pdb:6VXX) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the closed state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Interaction between the SARS-CoV-2 spike and the α7 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α7 nicotinic acetylcholine receptor. A7_nAChR-spike.tar.gz contains all the following files. A7_nAChR-spike_complex.pdb A7_nAChR-spike_r1.tpr A7_nAChR-spike_r1.xtc A7_nAChR-spike_r2.tpr A7_nAChR-spike_r2.xtc A7_nAChR-spike_r3.tpr A7_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A7_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub/MulhollandGroup/nAChR-spike_interaction/A7_nAChR-spike_complex.pdb
Models: ---

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (62 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

Riken CPR TMS, MD1_Up trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

Riken CPR TMS, MD2_Up trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

Trajectories of full-length SPIKE protein in the Open state. (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (166 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model (60 ns )

Dmitry Morozov
University of Jyvaskyla
This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The protein was solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.1Charmm27
Input and Supporting Files:

trimer

Trajectory: Get Trajectory (2.0 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: SARS-CoV-2 spike protein trimer (closed state) model for MD simulations

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulation was conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (49 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Inhibition of formation of the viral fusion core

SIRAH-CoV2 initiative - Glycosylated RBD (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike´s RBD glycosylated at Asn331 and Asn343. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI.

There are two different sets of simulations corresponding to Core Complex and High Mannose. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and RBD-Man9_SIRAHcg_rawdata_6-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Analogous information for Core-complex glycosylations is contained in files RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar.

Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in SIRAHcg_10us_prot.tar contains only the protein coordinates, while SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file RBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd RBD-Core-complex_SIRAHcg_prot.prmtop RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.ncrst RBD-Core-complex_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (16.4 GB)
Represented Proteins: spike RBD
Represented Structures: 6VSB
Models: ---

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Riken CPR TMS, TMD3_toDown trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Trajectories of full-length SPIKE protein in the Closed state. (1.7 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Closed state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (13 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Riken CPR TMS, MD2_Down trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

Riken CPR TMS, TMD2_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481 (10 µs )

Garay Pablo
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of a Spike’s RBD from SARS-CoV2 glycosylated at Asn331, 343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan were parameterized as reported in Garay et at. 2020.

The files 6XEY-RBD-3Man9_SIRAHcg_0-4us.tar, 6XEY-RBD-3Man9_SIRAHcg_4-8us.tar, and 6XEY-RBD-3Man9_SIRAHcg_8-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap the simulations. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file with names ending in 6XEY-RBD-3Man9_SIRAHcg_glycoprot_10us.tar contains only the protein coordinates, while 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar contains one frame every 10ns.

To take a quick look at a the trajectory:

1- Untar the file 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6XEY-RBD-3Man9_SIRAHcg_glycoprot.prmtop 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.ncrst 6XEY-RBD-3Man9_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (11.2 GB)
Represented Proteins: spike RBD
Represented Structures: 6XEY
Models: ---

1 microsecond trajecotry of glycosylated spike protein in open state for pdb:6VSB embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in open state (pdb:6VSB) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the open state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

Interaction between the SARS-CoV-2 spike and the αβγδ nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the αβγδ nicotinic acetylcholine receptor from Tetronarce californica (formerly Torpedo californica). ABGD_nAChR-spike.tar.gz contains the following files ABGD_nAChR-spike_complex.pdb ABGD_nAChR-spike_r1.tpr ABGD_nAChR-spike_r1.xtc ABGD_nAChR-spike_r2.tpr ABGD_nAChR-spike_r2.xtc ABGD_nAChR-spike_r3.tpr ABGD_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

ABGD_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/ABGD_nAChR-spike_complex.pdb
Models: ---

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

Trajectories of full-length SPIKE protein in the Open state (N165A / N234A mutations). (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state bearing N165A and N234A mutations, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

Riken CPR TMS, MD1_Down trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an inactive Down taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vxx
Models:

Riken CPR TMS, TMD1_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD2_toDown trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Up to Down forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vsb 6vxx
Models:

Riken CPR TMS, TMD3_toUp trajectory (50 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (38MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

Interaction between the SARS-CoV-2 spike and the α4β2 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α4β2 nicotinic acetylcholine receptor. A4B2_nAChR-spike.tar.gz contains the following files. A4B2_nAChR-spike_complex.pdb A4B2_nAChR-spike_r1.tpr A4B2_nAChR-spike_r1.xtc A4B2_nAChR-spike_r2.tpr A4B2_nAChR-spike_r2.xtc A4B2_nAChR-spike_r3.tpr A4B2_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A4B2_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/nAChR-spike_interaction/A4B2_nAChR-spike_complex.pdb
Models: ---

Folding@home simulations of the SARS-CoV-2 spike protein (1.2 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of the SARS-CoV-2 spike protein, simulated using Folding@Home. The dataset comprises 3 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14217) or OpenMM (PROJ14235 and PROJ14561) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14217 and PROJ14253 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14253 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14561 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/spike/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/spike/PROJ14217_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (6.5 TB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: ---

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (4.1 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

DESRES-ANTON-11021571 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in a partially opened state (PDB entry 6VYB). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021571-structure.tar.gz

DESRES-Trajectory_sarscov2-11021571.mp4

Trajectory: Get Trajectory (67 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

1 microsecond trajecotry of glycosylated spike protein in closed state for pdb:6VXX embedded in viral membrane (1 µs )

Klauda lab
All atom simulation of full-glycosylated spike protein in closed state (pdb:6VXX) embedded in viral membrane. The structure was taken from Charmm-Gui at http://www.charmm-gui.org/?doc=archive&lib=covid19 where 8 models were built for the closed state. For MD simulations we used model 1-2-1 provided by Im et. al. The PSF, PDB and XTC files are uploaded
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (12 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models:

Riken CPR TMS, MD2_Up trajectory (200 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (149MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

Trajectories of full-length SPIKE protein in the Open state. (4.2 µs )

Amaro Lab
All-atom MD simulations of full-length SPIKE protein in the Open state, protein + glycans only (not aligned). PSF and DCDs files are provided.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15CHARMM36
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike
Represented Structures: 6VSB
Models:

Interaction between the SARS-CoV-2 spike and the α7 nicotinic receptor (3 replicates, 300 ns each )

A.S.F. Oliveira
University of Bristol -- Mulholland Lab
MD simulation of the complex between the Y674-R685 region of the SARS-CoV-2 spike and the extracellular domain of the human α7 nicotinic acetylcholine receptor. A7_nAChR-spike.tar.gz contains all the following files. A7_nAChR-spike_complex.pdb A7_nAChR-spike_r1.tpr A7_nAChR-spike_r1.xtc A7_nAChR-spike_r2.tpr A7_nAChR-spike_r2.xtc A7_nAChR-spike_r3.tpr A7_nAChR-spike_r3.xtc
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.1Amber ff99SB-ILDN
Input and Supporting Files:

A7_nAChR-spike.tar.gz

Trajectory: Get Trajectory (9 GB)
Represented Proteins: spike
Represented Structures: https://molssi-bioexcel-covid-19-structure-therapeutics-hub/MulhollandGroup/nAChR-spike_interaction/A7_nAChR-spike_complex.pdb
Models: ---

DESRES-ANTON-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in a partially opened state (PDB entry 6VYB) which exhibited a high degree of conformational heterogeneity. In particular, the partially detached receptor binding domain sampled a variety of orientations, and further detached from the S2 fusion machinery. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439 for the closed state. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897850-structure.tar.gz

DESRES-Trajectory_sarscov2-10897850.mp4

Trajectory: Get Trajectory (62 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

Riken CPR TMS, MD1_Up trajectory (1 microseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Molecular Dynamics (MD) of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The starting structure is an active Up taken from CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19). We replaced counter ions K+ in the original model with Na+. The simulation used CHARMM36m force field for protein, and TIP3P water model. The simulation was performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Up_pro-gly.psf

Trajectory: Get Trajectory (742MB)
Represented Proteins: spike
Represented Structures: 6vsb
Models:

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (166 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model (60 ns )

Dmitry Morozov
University of Jyvaskyla
This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The protein was solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.1Charmm27
Input and Supporting Files:

trimer

Trajectory: Get Trajectory (2.0 GB)
Represented Proteins: spike
Represented Structures: 6VXX
Models: SARS-CoV-2 spike protein trimer (closed state) model for MD simulations

DESRES-ANTON-10897136 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation of the trimeric SARS-CoV-2 spike glycoprotein. System was initiated in the closed state (PDB entry 6VXX), which remained stable. The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502 for the closed state. The interval between frames is 1.2 ns. The simulation was conducted at 310 K in the NPT ensemble. We have released new versions of these simulations with enhancements to the spike protein model in [DESRES-ANTON-11021566,11021571] (https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/#DESRES-ANTON-11021566), since the one used in this simulation is incomplete in some of the disordered loop regions (i.e., resid 455 to 461, resid 469 to 488) and in glycan chains.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10897136-structure.tar.gz

DESRES-Trajectory_sarscov2-10897136.mp4

Trajectory: Get Trajectory (49 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Riken CPR TMS, TMD1_toUp trajectory (20 nanoseconds )

Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
RIKEN CPR (Cluster for Pioneering Research), TMS (Theoretical molecular science) laboratory -- TMS (Theoretical molecular science) laboratory
The data set includes a trajectory file from Targeted Molecular Dynamics (TMD) simulations of a fully glycosylated SARS-CoV-2 S-protein in solution. Water molecules and counter ions were excluded. The data includes trajectory from TMD simulation of Down to Up forms. The simulations used CHARMM36m force field for protein, and TIP3P water model. The simulations were performed using GENESIS. The coordinates were saved every 1 nanoseconds and aligned to S2 domain (Calpha atoms of residues 689-727, 854-1147).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310.15N/Awater0.15CHARMM36m
TIP3
Input and Supporting Files:

Down_pro-gly.psf

Trajectory: Get Trajectory (15MB)
Represented Proteins: spike
Represented Structures: 6vxx 6vsb
Models:

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

DESRES-ANTON-11021566 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains to improve the spike protein model originally released in DESRES-ANTON-[10897136,10897850]. Trajectory was initiated in the closed state (PDB entry 6VXX). The simulation used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-11021566-structure.tar.gz

DESRES-Trajectory_sarscov2-11021566.mp4

Trajectory: Get Trajectory (51 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

DESRES-ANTON-10906555 2 µs simulations of 50 FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein, no water or ions (2 µs )

D. E. Shaw Research
DESRES
50 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to a construct of the SARS-CoV-2 trimeric spike protein at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 50 putative spike protein binding small molecules located at three regions on the spike trimer, a pocket in the RBD whose formation may possibly enhance RBD-RBD interactions in the closed conformation (8 molecules), a pocket between the two RBDs in the closed conformation (29 molecules), and a pocket that involves three RBDs in the closed conformation (13 molecules). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The spike trimer construct was modeled from PDB entries 6VXX and 6VW1, only retaining the RBD and a short region from S1 fusion protein as a minimal system for maintaining a trimer assembly. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10906555-set_spike-structure.tar.gz

DESRES-Trajectory_sarscov2-10906555-set_spike-table.csv

DESRES-Trajectory_sarscov2-10906555.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: spike RBD
Represented Structures: 6vw1 6vxx
Models: SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

SIRAH-CoV2 initiative - S1 Receptor Binding Domain in complex with human antibody CR3022 (12 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycans have been removed from the structures.

The file 6W41_SIRAHcg_rawdata.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W41_SIRAHcg_12us_prot.tar contains only the protein coordinates, while 6W41_SIRAHcg_12us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W41_SIRAHcg_12us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6W41_SIRAHcg_prot.prmtop 6W41_SIRAHcg_prot_12us_skip10ns.ncrst 6W41_SIRAHcg_prot_12us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.6 GB)
Represented Proteins: spike RBD
Represented Structures: 6W41
Models: ---

SIRAH-CoV2 initiative - S2 Spike core fragment in postfusion state (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M1V_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot_10us_skip10ns.ncrst 6M1V_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (17.8 GB)
Represented Proteins: spike S2
Represented Structures: 6M1V
Models: ---

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2


Simulations of Viral Protease, Polymerase, and Nonstructured Proteins

SARS-CoV-2 main protease (3CLpro or NSP5)

3CLpro / Mpro activity

DESRES 100 µs MD of 3CLpro, no water or ions (100 µs )

D. E. Shaw Research
DESRES
This trajectory is from a 100 µs MD simulation of the apo enzyme started from the apo enzyme structure determined by X-ray crystallography (PDB entry 6Y84) The protein was solvated in a 120 x 120 x 120 Å water box containing 0.15 M NaCl. The simulation was performed on Anton 2 using the DES-Amber force field The interval between frames is 1 ns. The simulation was conducted in the NPT ensemble. This trajectory has been stripped of all waters and ions
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2981Water0.15DES-Amber FF
Input and Supporting Files: ---
Trajectory: Get Trajectory (9.6 GB)
Represented Proteins: 3CLpro
Represented Structures: 6Y84
Models: 3CLpro prepared for simulation in a 120 cubic A box for long continuous trajectory

DESRES 100 µs MD of 3CLpro, All Atom (100 µs )

D. E. Shaw Research
DESRES
This trajectory is from a 100 µs MD simulation of the apo enzyme started from the apo enzyme structure determined by X-ray crystallography (PDB entry 6Y84) The protein was solvated in a 120 x 120 x 120 Å water box containing 0.15 M NaCl. The simulation was performed on Anton 2 using the DES-Amber force field The interval between frames is 1 ns. The simulation was conducted in the NPT ensemble. This trajectory is all atom
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2981Water0.15DES-Amber FF
Input and Supporting Files: ---
Trajectory: Get Trajectory (216 GB)
Represented Proteins: 3CLpro
Represented Structures: 6Y84
Models: 3CLpro prepared for simulation in a 120 cubic A box for long continuous trajectory

HADDOCK docking of approved Drugbank set against Mpro with a pharmacophore shape model

P. I. Koukos, M. Réau, A. M. J. J Bonvin
Computational Structural Biology group, Bijvoet Centre for Biomolecular Research, Utrecht University
Repurposing study of the approved subset of Drugbank + active metabolites + investigational compounds of interest against Mpro. Compounds are guided to the binding site using 3D pharmacophore data extracted from a plethora of templates available on the PDB and also through the Diamond assay. The template compound shapes have been superimposed on the binding pocket of 6Y2F which is the receptor that was used for the docking. Ambiguous distance restraints are defined between target compound atoms and the template shape beads. Docking is performed in vacuum using the OPLS (UA) forcefield with a shifting function and a target of 8.5Å for the electrostatic energy and a switching function between 6.5 and 8.5Å for vdW energy, respectively. Compounds are scored using a scoring function comprised of the sum of vdW and electrostatics energies and an empirical desolvation potential.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingOtherN/AN/AvacuumN/AOPLS-UA
Input and Supporting Files:

README_mpro_pharmacophore.pdf

Trajectory: Get Trajectory (11 GB)
Represented Proteins: 3CLpro
Represented Structures: 6Y2F
Models: Truncated Mpro based on 6Y2F and pharmacophore-compliant 3D conformers

Riken BDR 10 Microsecond Trajectory System Snapshot every 10ns (10 µs )

Teruhisa S. Komatsu, Yohei M. Koyama, Noriaki Okimoto, Gentaro Morimoto, Yousuke Ohno, Makoto Taiji
Riken Biosystems Dynamics Research
Single 10 microseconds trajectory of SARS-CoV-2 dimeric main protease, NVT at 310K, with the time step 2.5fs (more precisely, 2.500000409 fs). The starting structure was prepared based on PDB 6LU7, with amber99sb-ildn force field. The system is composed of 98,694 atoms in 9.98921 nm length cubic box with periodic boundary conditions. Simulation performed in aqueous solution with solvent forcefield TIP3P.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310N/AWaterN/Aamber99sb-ildn
TIP3P
Input and Supporting Files:

sarscov2-10421220-structure.tar

Trajectory: Get Trajectory (343 MBs)
Represented Proteins: 3CLpro
Represented Structures: 6LU7
Models: SARS-CoV-2 dimeric main protease without ligand based on PDB 6LU7

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 1ns (10 µs )

Teruhisa S. Komatsu, Yohei M. Koyama, Noriaki Okimoto, Gentaro Morimoto, Yousuke Ohno, Makoto Taiji
Riken Biosystems Dynamics Research
Single 10 microseconds trajectory of SARS-CoV-2 dimeric main protease, NVT at 310K, with the time step 2.5fs (more precisely, 2.500000409 fs). The starting structure was prepared based on PDB 6LU7, with amber99sb-ildn force field. The system is composed of 98,694 atoms in 9.98921 nm length cubic box with periodic boundary conditions. Simulation performed in aqueous solution with solvent forcefield TIP3P.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310N/AWaterN/Aamber99sb-ildn
TIP3P
Input and Supporting Files:

sarscov2-10921231-structure.tar

Trajectory: Get Trajectory (340 MBs)
Represented Proteins: 3CLpro
Represented Structures: 6LU7
Models: SARS-CoV-2 dimeric main protease without ligand based on PDB 6LU7

11 ps QM/MM simulation of Transition State of SARS-CoV2 3CLpro (10 ps )

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón
Universidad de Valencia -- Efectos del medio
QM/MM Molecular Dynamics simulations of the Transition State obtained during the acylation reaction using the string method. QM/MM Free Energy simulations where made at the hybrid B3LYP/MM level including D3 dispersion corrections with the 6-31+G* basis set.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT300N/AWaterN/Aff14SB
TIP3P
GAFF
Input and Supporting Files: ---
Trajectory: Get Trajectory (1 GB)
Represented Proteins: 3CLpro
Represented Structures: https://www.rcsb.org/structure/7BQY
Models:

Simulation files for docking the SARS-CoV Mpro natural substrate to an Mpro target using NarupaIMD

Rebecca K. Walters
University of Bristol -- Intangible Realities Laboratory
Relevant smulation files in order to set-up a Narupa IMD simulation for docking the N-terminal natural substrate to three different Mpro targets (i) SARS-CoV Mpro, (ii) an Apo SARS-CoV-2 Mpro, and (iii) an Inhibitor complexed SARS-CoV-2 Mpro (where the inhibitor was deleted from the active site prior to docking). There are 6 simulations files in total. Documentation detailing how to set up a NarupaIMD simulation using these files can be found [here] (https://gitlab.com/intangiblerealities/narupa-applications/narupa-imd)
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingNVT300N/AOBC2N/Aff14SB
Input and Supporting Files: ---
Trajectory: Get Trajectory (45 MB)
Represented Proteins: 3CLpro
Represented Structures: https://www.rcsb.org/structure/6M03
Models:

SIRAH-CoV2 initiative - Main Protease (15 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 15 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Main protease in its APO form (PDB id: 6LU7, Bioassembly 1). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6LU7_SIRAHcg_rawdata1.tar, 6LU7_SIRAHcg_rawdata2.tar, and 6LU7_SIRAHcg_rawdata3.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6LU7_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6LU7_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: bash vmd 6LU7_SIRAHcg_prot.prmtop 6LU7_SIRAHcg_prot_15us_skip10ns.ncrst 6LU7_SIRAHcg_prot_15us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (18 GB)
Represented Proteins: 3CLpro
Represented Structures: 6LU7
Models: ---

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 200ps (10 µs )

Teruhisa S. Komatsu, Yohei M. Koyama, Noriaki Okimoto, Gentaro Morimoto, Yousuke Ohno, Makoto Taiji
Riken Biosystems Dynamics Research
Single 10 microseconds trajectory of SARS-CoV-2 dimeric main protease, NVT at 310K, with the time step 2.5fs (more precisely, 2.500000409 fs). The starting structure was prepared based on PDB 6LU7, with amber99sb-ildn force field. The system is composed of 98,694 atoms in 9.98921 nm length cubic box with periodic boundary conditions. Simulation performed in aqueous solution with solvent forcefield TIP3P.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT310N/AWaterN/Aamber99sb-ildn
TIP3P
Input and Supporting Files:

sarscov2-10921231-structure.tar

Trajectory: Get Trajectory (1.7 GBs)
Represented Proteins: 3CLpro
Represented Structures: 6LU7
Models: SARS-CoV-2 dimeric main protease without ligand based on PDB 6LU7

HADDOCK docking of approved Drugbank set against Mpro with a geometric shape model

P. I. Koukos, M. Réau, A. M. J. J Bonvin
Computational Structural Biology group, Bijvoet Centre for Biomolecular Research, Utrecht University
Repurposing study of the approved subset of Drugbank + active metabolites + investigational compounds of interest against Mpro. Compounds are guided to the binding site using 3D shape data extracted from a plethora of templates available on the PDB and also through the Diamond assay. The template compound shapes have been superimposed on the binding pocket of 6Y2F which is the receptor that was used for the docking. Ambiguous distance restraints are defined between target compound atoms and the template shape beads. Docking is performed in vacuum using the OPLS (UA) forcefield with a shifting function and a target of 8.5Å for the electrostatic energy and a switching function between 6.5 and 8.5Å for vdW energy, respectively. Compounds are scored using a scoring function comprised of the sum of vdW and electrostatics energies and an empirical desolvation potential.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingOtherN/AN/AvacuumN/AOPLS-UA
Input and Supporting Files:

README_mpro_tanimoto.pdf

Trajectory: Get Trajectory (11 GB)
Represented Proteins: 3CLpro
Represented Structures: 6Y2F
Models: Truncated Mpro based on 6Y2F and shape-compliant 3D conformers

Simulation files for docking a small molecule inhibitor (X77) to an Mpro target using NarupaIMD

Helen M. Deeks
University of Bristol -- Intangible Realities Laboratory
Relevant smulation files in order to set-up a Narupa IMD simulation for docking a small molecule inhibitor (X77) to two different Mpro targets (i) an Apo SARS-CoV-2 Mpro, and (ii) an Inhibitor complexed SARS-CoV-2 Mpro. There are 2 simulations files in total. Documentation detailing how to set up a NarupaIMD simulation using these files can be found [here] (https://gitlab.com/intangiblerealities/narupa-applications/narupa-imd)
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingNVT300N/AOBC2N/Aff14SB
GAFF
Input and Supporting Files: ---
Trajectory: Get Trajectory (19 MB)
Represented Proteins: 3CLpro
Represented Structures: https://www.rcsb.org/structure/6W63
Models:

Folding@home SARS-CoV-2 main protease (apo, monomer) simulations (2.6 ms )

Rafal Wiewiora
Folding@home -- Chodera lab

This is a dataset containing 5688 trajectories at least 250 ns in length (2.6 ms in total) of the SARS-CoV-2 main viral protease (Mpro/3CLpro) in its apo, monomeric form with neutral His41 and Cys145. Water (but not salt) has been stripped from the trajectories, and frames are saved every 0.2 ns. Simulations were initiated from PDB structure 6lu7, chain A, after removing the inhibitor and structural waters. The dataset is organized by Folding@home project number (11743 and 11749) due to the F@h parallelization – there are no differences in setups between the projects and there is no relation between the identically named files - all trajectories (CLONEs) are initialized with random velocities. Chain A (i.e. a monomer of the protein, without the inhibitor or waters) was extracted from 6lu7 using PyMOL, and protonated and capped (ACE, NME) with Schrodinger’s Maestro. The model can be downloaded here. Simulations were performed in the NPT ensemble (310 K, 1 atm), in a cubic box with 1 nm padding, 150 mM NaCl, with hydrogen mass repartitioning (4 amu H mass), using amber14SB and tip3p forcefields. OpenMM 7.4.1 was used. System was equilibrated for 5 ns using 2 fs timestep with default OpenMM Langevin integrator, then for 1.25 ns using 4 fs timestep with OpenMMTools custom Langevin integrator using V R O R V splitting. All Folding@home trajectories were then seeded with random velocities from this system. The dataset is available through the AWS Open Data Registry and can be retrieved through the AWS CLI: To download the whole dataset (519 GB):

aws s3 sync --no-sign-request s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2_main_protease_monomer .

To download subsets of the dataset appropriate query terms can be used. For example, to retrieve the first trajectory of project 11743: bash aws s3 cp --no-sign-request s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2_main_protease_monomer/11743/run0-clone0.h5 . the first 10 trajectories of project 11743: bash aws s3 sync --no-sign-request --exclude "*" --include "11743/run0-clone?.h5" s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2_main_protease_monomer . the first 100 trajectories of project 11743: bash aws s3 sync --no-sign-request --exclude "*" --include "11743/run0-clone??.h5" s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2_main_protease_monomer .

Individual files can also be downloaded directly via HTTP, for example. If you have an AWS account, data can also be browsed and downloaded via the [AWS Management Console(https://s3.console.aws.amazon.com/s3/buckets/fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2_main_protease_monomer). This dataset is also available through the Open Science Framework.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15amber14SB
tip3p
Input and Supporting Files:

6lu7_receptor

Trajectory: Get Trajectory (519.1 GB)
Represented Proteins: 3CLpro
Represented Structures: 6LU7
Models: SARS-CoV-2 main protease (apo, monomer) for Folding@home simulations

Folding@home simulations of nsp5 (2.9 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp5, simulated using Folding@Home. The dataset comprises 4 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14234 and PROJ14542 and PROJ14584) or OpenMM (PROJ14543) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14234 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/PROJ14234 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/PROJ14542 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/PROJ14584 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/PROJ14543 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp5_dimer/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp5_dimer/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/PROJ14234_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_dimer/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: 3CLpro
Represented Structures: 6Y2E
Models: ---

6.95 us simulation of SARS-CoV2 3CLpro in complex with the N3 inhibitor all atom simulation (6.5 us )

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón
Universidad de Valencia -- Efectos del medio
6.5 us Molecular Dynamics simulations of the non-covalent enzyme-inhibitor (EI) complex built from the 7BQY PDB structure
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNVT300N/AWaterN/Aff14SB
TIP3P
GAFF
Input and Supporting Files: ---
Trajectory: Get Trajectory (577 MB)
Represented Proteins: 3CLpro
Represented Structures: https://www.rcsb.org/structure/7BQY
Models:

Folding@home simulations of nsp5 (6.4 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp5, simulated using Folding@Home. The dataset comprises 4 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14582, PROJ14592, and PROJ16411) or OpenMM (PROJ16435) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14592 and PROJ16411 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ14582 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ14592 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ16411 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ16435 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp5_monomer/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp5_monomer/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ14592_tpr_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/PROJ16411_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp5_monomer/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: 3CLpro
Represented Structures: 6Y2E
Models: ---

Folding@home expanded ensemble absolute free energy calculations of potential small molecule inhibitors of the SARS-CoV-2 main protease from the COVID Moonshot (5.2 ms )

Matt Hurley
Folding@home -- Voelz lab

This dataset contains all-atom expanded ensemble absolute free calculations for potential small molecule inhibitors of the SARS-CoV-2 main viral protease (Mpro, 3CLpro) from the COVID Moonshot simulated on Folding@home with gromacs.

Molecules from datasets prefixed with “MS” were crowdsourced small molecule designs submitted to the COVID Moonshot.

Each small molecule was run alone in solution and docked to Mpro to compute absolute free energies of binding. Simulations were run using GROMACS-5.0.4 or GROMACS-2020 and are stored as compressed binary XTC files. Absolute free energies were computed using an expanded ensemble scheme, using 40 lambdas to decouple the ligand interactions. Free energy data for each alchemical lambda is stored in the md.log file, and found more concisely in pre-scraped pickle (.pkl) dataframes. The dataset comprises several projects, each having a RUN*/CLONE*/result* directory structure:

  • each PROJ represents a different dataset of small molecules
  • each RUN represents a different small molecule
  • each CLONE is a unique MD simulation differing in initial atomic velocities
  • each result* is a fragment of the contiguous simulation

For the case of ligand-only “L” simulations, each XTC represents 10ns of sampling, while each complex “RL” xtc trajectory is only 1 ns. More information about the simulation set-up can be found here. In order to find particular PROJ/RUN of interest, see the results and organization dataframes.

Organization dataframe: In order to determine systems of interest, you can parse this dataframe which contains information on which ligands are present in each project/run. Half of the projects contain trajectories for ligands alone in solution, while the other half contain trajectories for ligands docked to the main protease. More data is being added to this repository every day, so if a project/run is not available in the AWS bucket, check back later or contact Matt Hurley.

Topology files: Structure and topology files corresponding to each run can be found in the build directories. All-atom files that include solvent and ions are named npt.gro, while files containing only protein and ligand information are named xtc.gro. Other files of interest include the force-field parameters, stored in topol.top, and prod.mdp, which holds the MD parameters for running expanded ensemble simulations. The dataset is available through the AWS Open Data Registry and can be retrieved through the AWS CLI. For example, to retrieve the whole project 14721:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/build/p14721 .

To retrieve a a specific RUN (RUN0):

aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/build/p14722/RUN0 .

To retrieve a specific pair of .gro files from specific RUNs:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/build/p14725/RUN10/npt.gro .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-asbolute-free-energy/build/p14727/RUN20/xtc.gro .

Raw datasets: To get the raw trajectory files gromacs XTC format for the whole dataset (~10+ TB/PROJect), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14721 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14722/RUN2 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14725/RUN2/CLONE1 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14727/RUN2/CLONE1/results0 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14728/RUN2/CLONE1/results0/traj_comp.xtc .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/SVR51748107/PROJ14752/RUN5/CLONE0/results1/traj.trr .

Results dataframes: Compiled free energy results, extracted from each work unit’s log file can be found in the free-energy-data path. These dataframes are organized by dataset and contain the corresponding project number for accessing the raw data.

A pandas dataframe containing the most recently computed free energies of binding can be downloaded: results.pkl

All other dataframes can be downloaded using [AWS CLI[(https://aws.amazon.com/cli):

aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/free-energy-data .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/free-energy-data/MS0406-2_RL_14728.pkl .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-absolute-free-energy/free-energy-data/MS0406-2_L_14380.pkl .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT298.151water0.1AMBER14
TIP3P
OpenFF-1.2.0
Input and Supporting Files: ---
Trajectory: Get Trajectory (34 TB)
Represented Proteins: 3CLpro
Represented Structures: 6Y84
Models: SARS-CoV-2 main protease model for MD simulations

Folding@home molecular dynamics simulations of Diamond Light Source / XChem X-ray structures of small molecule inhibitors of the SARS-CoV-2 main protease from the COVID Moonshot (8 ms )

John D. Chodera
Folding@home -- Chodera lab

This dataset contains all-atom molecular dynamics simulations starting from Diamond Light Source / XChem X-ray structures of small molecule inhibitors of the SARS-CoV-2 main viral protease (Mpro, 3CLpro) from the COVID Moonshot simulated on Folding@home with gromacs.

All X-ray structures come from the XChem Fragalysis platform as of 2020-12-21. These structures are linked to activity data on the COVID Moonshot Structures browser.

All X-ray structures are simulated in multiple variants, each organized into a different Folding@home project number:

13430 : apo Mpro monomer His41(0) Cys145(0)
13431 : apo Mpro monomer His41(+) Cys145(-)
13432 : holo Mpro monomer His41(0) Cys145(0)
13433 : holo Mpro monomer His41(+) Cys145(-)
13434 : apo Mpro dimer His41(0) Cys145(0)
13435 : apo Mpro dimer His41(+) Cys145(-)
13436 : holo Mpro dimer His41(0) Cys145(0)
13437 : holo Mpro dimer His41(+) Cys145(-)

There are 356 X-ray structures as different RUNs within each PROJect, and 10 CLONEs within each RUN. Each CLONE will be terminated at 1 microsecond, producing an aggregate total of 8 ms of data.

NOTE: This dataset will continue to be populated for the next few weeks. Trajectories have not yet reached the full 1 microsecond/trajectory, but the available data is already useful for analysis.

Structures were prepared with SpruceTK from the OpenEye Toolkit 2020.1.0 using the scripts in the covid-moonshot repo. Simulations were run with the OpenMM 7.4.2 (Folding@home core22 0.0.14). Solute snapshots were saved every 1 ns.

The dataset comprises several projects, each having a RUN*/CLONE*/result* directory structure:

  • each PROJ represents a different dataset of small molecules
  • each RUN represents a different small molecule
  • each CLONE is a unique MD simulation differing in initial atomic velocities
  • each result* is a 20 ns fragment of the contiguous simulation

Project index: An index of all the projects can be found here. A CSV file indexing all the fragments (in terms of Folding@home RUNs) can be found here: fah-metadata.csv Continuous solute-only trajectories: To download all the protein-ligand trajectories in MDTraj HDF5 format, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2-Mpro-Diamond-structures/solute-hdf5-trajectories .

To download a single trajectory, you can specify the path to the PROJECT (assembly state), RUN (ligand index), and CLONE (replicate). For example, to retrieve the holo (ligand-bound) Mpro dimer with His41(+) Cys145(-) (charged catalytic dyad) for ligand 0 (x11271):

aws s3 --no-sign-request cp s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2-Mpro-Diamond-structures/solute-hdf5-trajectories/13437/run0-clone0.h5 .

MDTraj HDF5 files contain the topology, so you can use the conda- and pip-installable MDTraj to convert to the desired format (PDB, XTC, DCD, etc.) or slice out specific frames programmatically. MDTraj also provides the mdconvert tool to do this from the command line. For example, to generate a PDB of the first frame and an XTC file of all the frames:

mdconvert run0-clone0.h5 --index 0 -o run0-clone0.pdb
mdconvert run0-clone0.h5 -o run0-clone0.xtc

*Retrieving all data: You can retrieve the whole dataset with:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-moonshot-dynamics/SARS-CoV-2-Mpro-Diamond-structures .

This contains

setup/ - input OpenMM XML and PDB files used to run simulations with Folding@home OpenMM core
solute-hdf5-trajectories/ - concatenated MDTraj HDF5 files with topology information
project-data/ - raw XTC file output from Folding@home work units
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.07AMBER14SB
TIP3P
OpenFF-1.3.0
Input and Supporting Files: ---
Trajectory: Get Trajectory (175.1 GB)
Represented Proteins: 3CLpro
Represented Structures: ---
Models: ---


SARS-CoV-2 Macrodomain (NSP3)

Host immune response

SIRAH-CoV2 initiative - Apo ADP-ribose phosphatase of NSP3 (10 µs )

Exequiel Barrera
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 ADP ribose phosphatase of NSP3 from SARS CoV-2 in its APO form (PDB id: 6W02, Bioassembly 1). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6W02_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W02_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W02_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W02_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W02_SIRAHcg_prot.prmtop 6W02_SIRAHcg_prot_10us_skip10ns.ncrst 6W02_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.4 GB)
Represented Proteins: Macrodomain
Represented Structures: 6W02
Models: ---

Folding@home simulations of nsp3 macrodomain (11 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp3 macrodomain, simulated using Folding@Home. The dataset comprises 4 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14576 and PROJ14593) or OpenMM (PROJ14541 and PROJ14564) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14593 and PROJ14564 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/PROJ14576 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/PROJ14593 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/PROJ14541 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/PROJ14564 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp3_X/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp3_X/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/PROJ14593_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_X/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: Macrodomain
Represented Structures: 6W02
Models: ---


SARS-CoV-2 Papain-like protease (NSP3)

Inhibition of PLpro protease activity

Apo SARS-CoV-2 PLPro (from PDB 6WRH C-chain) (1 μs )

Chia-en A. Chang, Yuliana Bosken, Timothy Cholko
Chang group, University of California, Riverside
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped water molecules and counter ions.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2980.987WaterN/AFF14SB
Input and Supporting Files:

md_input.zip

Trajectory: Get Trajectory (5.5GB)
Represented Proteins: PLpro
Represented Structures: 6wrh
Models: SARS-CoV-2 ligand-free (PDB 6WRH)

SIRAH-CoV2 initiative - Papain-like Protease (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6W9C_SIRAHcg_rawdata_0-5us.tar and 6W9C_SIRAHcg_rawdata_5-10us.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W9C_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W9C_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W9C_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot_10us_skip10ns.ncrst 6W9C_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (13 GB)
Represented Proteins: PLpro
Represented Structures: 6W9C
Models: ---

Apo SARS-CoV PLpro (1 μs )

Chia-en A. Chang, Yuliana Bosken, Timothy Cholko
Chang group, University of California, Riverside
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2980.987WaterN/AFF14SB
Input and Supporting Files:

md_input.zip

Trajectory: Get Trajectory (5.4GB)
Represented Proteins: PLpro
Represented Structures: 4ow0
Models: SARS-CoV-1 ligand-free (PDB 4OW0 ligand removed)

Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain) (1 μs )

Chia-en A. Chang, Yuliana Bosken, Timothy Cholko
Chang group, University of California, Riverside
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped water molecules and counter ions.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2980.987WaterN/AFF14SB
Input and Supporting Files:

md_input.zip

Trajectory: Get Trajectory (5.5GB)
Represented Proteins: PLpro
Represented Structures: 6w9c
Models: SARS-CoV-2 ligand-free (PDB 6W9C - chain C)

Folding@home simulations of nsp3 pl2pro domain (731 µs )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp3 pl2pro, simulated using Folding@Home. The dataset comprises 2 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ14589 and PROJ14548) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ14548 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_pl2pro/PROJ14589 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_pl2pro/PROJ14548 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp3_pl2pro/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp3_pl2pro/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_pl2pro/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_pl2pro/PROJ14548_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp3_pl2pro/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: PLpro
Represented Structures: 3E9S
Models: ---

3k bound SARS-CoV PLPro (1 μs )

Chia-en A. Chang, Yuliana Bosken, Timothy Cholko
Chang group, University of California, Riverside
1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped water molecules and counter ions.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2980.987WaterN/AFF14SB
GAFF2
Input and Supporting Files:

md_input.zip

Trajectory: Get Trajectory (5.4GB)
Represented Proteins: PLpro
Represented Structures: 4ow0
Models: SARS-CoV-1 ligand-bound (PDB 4OW0)

3k bound SARS-CoV-2 PLPro (3k docked to frame from trajectory of PDB 6W9C C-chain) (1 μs )

Chia-en A. Chang, Yuliana Bosken, Timothy Cholko
Chang group, University of California, Riverside
1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped water molecules and counter ions.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT2980.987WaterN/AFF14SB
GAFF2
Input and Supporting Files:

md_input.zip

Trajectory: Get Trajectory (5.4GB)
Represented Proteins: PLpro
Represented Structures: 6w9c
Models: SARS-CoV-2 ligand-bound (3k ligand was docked to protein conformation from 6W9C ligand-free MD)


SARS-CoV-2 RNA Polymerase (NSP12)

Inhibition of viral polymerases

SIRAH-CoV2 initiative - RNA-dependent RNA polymerase in complex with cofactors NSP7 and NSP8 (10 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot_10us_skip10ns.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.8 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 7BTF
Models: ---

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model (300 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 300 ns atomic MD simulation of the SARS-CoV-2 RdRp apo-protein model. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 400 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

apo-RdRp

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.2 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV1
Models: SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-RTP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-RTP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (22 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-ATP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-ATP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6NUR 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

Folding@home simulations of nsp12 (3.4 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp12, simulated using Folding@Home. The dataset comprises 1 project, having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ16424) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16424 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp12/PROJ16424 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp12/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered ryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp12/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp12/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp12/PROJ16424_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp12/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: RdRP
Represented Structures: 6NUR
Models: ---

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (1.7 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

HADDOCK docking of approved Drugbank set against RdRp

P. I. Koukos, M. Réau, A. M. J. J Bonvin
Computational Structural Biology group, Bijvoet Centre for Biomolecular Research, Utrecht University
Repurposing study of the approved subset of Drugbank + active metabolites + investigational compounds of interest against RdRp. Compounds are guided to the binding site using restraints extracted from PDB id 7BV2. The binding sire residues have been defined using a distance cut-off of 5Å. Docking is performed in vacuum using the OPLS (UA) forcefield with a shifting and switching function for vdW and electrostatics energies, respectively. Scaling of intermolecular energies was lowered to 1/1000 of their original values for the initial rigid-body docking stage to allow the compounds to more easily penetrate into the binding pocket. Compounds are scored using a scoring function comprised of the sum of vdW and electrostatics energies and an empirical desolvation potential. respectively.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingOtherN/AN/AvacuumN/AOPLS-UA
Input and Supporting Files:

README_rdrp.pdf

Trajectory: Get Trajectory (25 GB)
Represented Proteins: RdRP
Represented Structures: 7BV2
Models: Docking-based repurposing study of approved drugs against truncated RdRp

No Targets Recorded


Helicase coronavirus nonstructural protein 13 (NSP13)

Inhibition of nsp13 helicase activity

Folding@home simulations of nsp13 (3.4 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp13, simulated using Folding@Home. The dataset comprises 2 project, having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ16419, and PROJ16420) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16420 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp13/PROJ16419 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp13/PROJ16420 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp13/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered ryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp13/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp13/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp13/PROJ16420_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp13/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: Helicase
Represented Structures: 6JYT
Models: ---

SIRAH-CoV2 initiative - Helicase (10 µs )

Pablo Garay
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Helicase protein (PDB id:6ZSL). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The file 6ZSL_SIRAHcg_rawdata_0-4us.tar, 6ZSL_SIRAHcg_rawdata_4-8us.tar, and 6ZSL_SIRAHcg_rawdata_8-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file **6ZSL_SIRAHcg_10us_prot.tar ** contains only the protein coordinates, while 6ZSL_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6ZSL_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6ZSL_SIRAHcg_prot.prmtop 6ZSL_SIRAHcg_prot_10us_skip10ns.ncrst 6ZSL_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (12.5 GB)
Represented Proteins: Helicase
Represented Structures: 6ZSL
Models: ---


Coronavirus nonstructural protein 1


Coronavirus nonstructural protein 10

No Targets Recorded

Folding@home simulations of nsp10 (6.1 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp10, simulated using Folding@Home. The dataset comprises 2 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ16402 and PROJ16403) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16403 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp10/PROJ14602 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp10/PROJ14603 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp10/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered ryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp10/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp10/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp10/PROJ16403_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp10/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: NSP10
Represented Structures: 6W4H
Models: ---

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 NSP16 - NSP10 Complex with Zn ions bound (PDB id: 6W4H). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The file 6W4H_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 6W4H_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W4H_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W4H_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W4H_SIRAHcg_prot.prmtop 6W4H_SIRAHcg_prot_10us_skip10ns.ncrst 6W4H_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (7.9 GB)
Represented Proteins: NSP16 NSP10
Represented Structures: 6W4H
Models: ---


Coronavirus nonstructural protein 11


Coronavirus nonstructural protein 14


Coronavirus nonstructural protein 15

No Targets Recorded

SIRAH-CoV2 initiative - NSP15 Endonuclease (10 µs )

Exequiel Barrera
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Endoribonuclease NSP15 in its APO form (PDB id: 6W01, Bioassembly 1). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6W01_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W01_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W01_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W01_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W01_SIRAHcg_prot.prmtop 6W01_SIRAHcg_prot_10us_skip10ns.ncrst 6W01_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (18.8 GB)
Represented Proteins: NSP15
Represented Structures: 6W01
Models: ---


Coronavirus nonstructural protein 16

No Targets Recorded

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 NSP16 - NSP10 Complex with Zn ions bound (PDB id: 6W4H). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The file 6W4H_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 6W4H_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W4H_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W4H_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W4H_SIRAHcg_prot.prmtop 6W4H_SIRAHcg_prot_10us_skip10ns.ncrst 6W4H_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (7.9 GB)
Represented Proteins: NSP16 NSP10
Represented Structures: 6W4H
Models: ---


Coronavirus nonstructural protein 2


Coronavirus nonstructural protein 4


Coronavirus nonstructural protein 6


Coronavirus nonstructural protein 7

Inhibition of viral polymerases

SIRAH-CoV2 initiative - Co-factor complex of NSP7 and the C-terminal domain of NSP8 (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot_10us_skip10ns.ncrst 6WIQ_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (11.4 GB)
Represented Proteins: NSP7 NSP8
Represented Structures: 6WIQ
Models: ---

Folding@home simulations of nsp7 (3.7 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp7, simulated using Folding@Home. The dataset comprises 2 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ16425) or OpenMM (PROJ16433) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16425 was seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp7/PROJ16425 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp7/PROJ16433 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp7/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp7/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp7/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp7/PROJ16425_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp7/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: NSP7
Represented Structures: 5F22
Models: ---

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-RTP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-RTP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (22 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

SIRAH-CoV2 initiative - NSP7-NSP8 complex (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 nsp7-nsp8 complex (PDB id: 6YHU, Bioassembly 1). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6YHU_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6YHU_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6YHU_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6YHU_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6YHU_SIRAHcg_prot.prmtop 6YHU_SIRAHcg_prot_10us_skip10ns.ncrst 6YHU_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (4.8 GB)
Represented Proteins: NSP7 NSP8
Represented Structures: 6YHU
Models: ---

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-ATP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-ATP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6NUR 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (1.7 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

SIRAH-CoV2 initiative - RNA-dependent RNA polymerase in complex with cofactors NSP7 and NSP8 (10 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot_10us_skip10ns.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.8 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 7BTF
Models: ---

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model (300 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 300 ns atomic MD simulation of the SARS-CoV-2 RdRp apo-protein model. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 400 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

apo-RdRp

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.2 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV1
Models: SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

No Targets Recorded


Coronavirus nonstructural protein 8

Inhibition of viral polymerases

SIRAH-CoV2 initiative - RNA-dependent RNA polymerase in complex with cofactors NSP7 and NSP8 (10 µs )

Martin Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot_10us_skip10ns.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.8 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 7BTF
Models: ---

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model (300 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 300 ns atomic MD simulation of the SARS-CoV-2 RdRp apo-protein model. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 400 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

apo-RdRp

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.2 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV1
Models: SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

Folding@home simulations of nsp8 (1.8 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp8, simulated using Folding@Home. The dataset comprises 2 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ16431) or OpenMM (PROJ16434) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16431 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp8/PROJ16431 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp8/PROJ16434 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp8/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp8/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp8/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp8/PROJ16431_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp8/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: NSP8
Represented Structures: 2AHM
Models: ---

SIRAH-CoV2 initiative - Co-factor complex of NSP7 and the C-terminal domain of NSP8 (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot_10us_skip10ns.ncrst 6WIQ_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (11.4 GB)
Represented Proteins: NSP7 NSP8
Represented Structures: 6WIQ
Models: ---

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-RTP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-RTP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (22 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model (100 ns )

Vaibhav Modi
University of Jyväskylä
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-ATP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15Amber14sb-OL15
Input and Supporting Files:

RdRp-RNA-ATP-complex

amber14sb_OL15.ff

Trajectory: Get Trajectory (1.5 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6NUR 6M71 7BTF 7BV2 6YYT
Models: SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

SIRAH-CoV2 initiative - NSP7-NSP8 complex (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 nsp7-nsp8 complex (PDB id: 6YHU, Bioassembly 1). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6YHU_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6YHU_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6YHU_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6YHU_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6YHU_SIRAHcg_prot.prmtop 6YHU_SIRAHcg_prot_10us_skip10ns.ncrst 6YHU_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (4.8 GB)
Represented Proteins: NSP7 NSP8
Represented Structures: 6YHU
Models: ---

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc (10 µs )

D. E. Shaw Research
DESRES
A 10 µs simulation trajectory of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex determined in the absence of reducing agent (PDB entry 6M71). In the simulation, the partially disordered N-terminal region (residue 30 to residue 120) of the NiRAN domain folded into a stable ordered structure that resembles the N-lobe fold of protein kinases. Lys 73 in β3 forms a salt bridge with Glu 83 in αC for most of the simulation, a common feature of protein kinases. The protein kinase-like fold formed in simulation is in good agreement with the structure of the same complex determined in the presence of reducing agent (PDB entry 7BTF). Structural comparison shows that the protein kinase-like fold in the NiRAN domain shares high similarity with that of the bacterial protein SELO, a protein kinase that catalyzes the transfer of adenosine 5’-monophosphate (AMP) to Ser, Thr and Tyr residues of target proteins, consistent with a potential connection between SELO and SARS-CoV-1 nps12 noted in a previous study. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water. The C- and N-peptide termini capped with amide and acetyl groups respectively. The missing loops in the published structural models were manually built as extended peptide conformation. The missing part of Chain D was built through homology modeling using the structure of SARS-CoV-1 polymerase complex (PDB entry 6NUR). The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted in the NPT ensemble. The structural similarity search was done using the DALI server, and the SELO structure (PDB entry 6EAC) was the highest ranked protein in the list.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10917618-structure.tar.gz

DESRES-Trajectory_sarscov2-10917618.mp4

Trajectory: Get Trajectory (1.7 GB)
Represented Proteins: RdRP NSP7 NSP8
Represented Structures: 6m71
Models: SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

No Targets Recorded


Coronavirus nonstructural protein 9

No Targets Recorded

SIRAH-CoV2 initiative - NSP9 RNA binding protein (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 NSP9 RNA binding protein (PDB id: 6W4B, Bioassembly 1). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6W4B_SIRAHcg_rawdata1.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W4B_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W4B_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W4B_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W4B_SIRAHcg_prot.prmtop 6W4B_SIRAHcg_prot_10us_skip10ns.ncrst 6W4B_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (6.0 GB)
Represented Proteins: NSP9
Represented Structures: 6W4B
Models: ---

Folding@home simulations of nsp9 (9 ms )

Maxwell Zimmerman
Folding@home -- Bowman lab

All-atom MD simulations of nsp9, simulated using Folding@Home. The dataset comprises 2 projects, each having a RUN*/CLONE*/result* directory structure. Simulations were run using GROMACS (PROJ13851, PROJ16423) and are stored as compressed binary XTC files. Each RUN represents a unique starting conformation, each CLONE is a unique MD run from the specified starting conformation, and each result is a fragment of the contiguous simulation. PROJ16423 were seeded using FAST simulations.

Topology files: The topology used in the trajectories can be downloaded directly here: PDB.

Entire dataset: The dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. To retrieve raw trajectory files in gromacs XTC format for the whole dataset, you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp9/PROJ13851 .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp9/PROJ16423 .

Markov State Model: A polished Markov State Model (MSM), including representative cluster centers, transition probabilities, and equilibrum populations, can be downloaded using the AWS CLI. Details of how the MSM model was constructed can be found here.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp9/model .

MSM cluster centers can be obtained as a gromacs XTC file from this URL: cluster centers XTC

Discovered cryptic pockets: Full description of the discovered cryptic pockets can be downloaded using the AWS CLI.

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/final_models/nsp9/cryptic_pockets .

Input files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp9/input_files .
aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp9/PROJ16423_tpr_files .

FAST simulations: FAST simulations, which were used as seeds for Folding@Home simulations, can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-cryptic-pockets/SARS-CoV-2/nsp9/FAST_simulations .
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.1AMBER03
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (O(1 TB))
Represented Proteins: NSP9
Represented Structures: 6W4B
Models: ---


Simulations of Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10


Coronavirus Open Reading Frame 3a

No Targets Recorded

SIRAH-CoV2 initiative - Membrane embedded ORF3a (10 µs )

Exequiel Barrera
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a dimeric transmembrane protein (PDB id: 6XDC, Bioassembly 1) embedded in a membrane patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Barrera et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The files 6XDC_SIRAHcg_rawdata_0-2us.tar, 6XDC_SIRAHcg_rawdata_2-4us.tar, 6XDC_SIRAHcg_rawdata_4-6us.tar, 6XDC_SIRAHcg_rawdata_6-8us.tar, and 6XDC_SIRAHcg_rawdata_8-10us.tar contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar contains only the protein and phospholipids´ coordinates, with one frame every 10ns. To take a quick look at the trajectory:

1- Untar the file 6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6XDC_SIRAHcg_prot-memb_skip10ns.prmtop 6XDC_SIRAHcg_prot-memb_10us_skip10ns.ncrst 6XDC_SIRAHcg_prot-memb_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (43 GB)
Represented Proteins: ORF3a
Represented Structures: 6XDC
Models: ---


Coronavirus Open Reading Frame 6


Coronavirus Open Reading Frame 7a

No Targets Recorded

SIRAH-CoV2 initiative - ORF7A enconded accessory protein (10 µs )

Martín Soñora
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 ORF7a encoded accessory protein (PDB id: 6W37). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6W37_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6W37_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W37_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W37_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6W37_SIRAHcg_prot.prmtop 6W37_SIRAHcg_prot_10us_skip10ns.ncrst 6W37_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.7 GB)
Represented Proteins: ORF7a
Represented Structures: 6W37
Models: ---


Coronavirus Open Reading Frame 7b


Coronavirus Open Reading Frame 8


Simulations of Viral Membrane Proteins

Membrane Glycoprotein


Simulations of Viral Envelope Proteins

Envelope small membrane protein


Simulations of Viral Nucleocapsid Proteins

Nucleoprotein

No Targets Recorded

SIRAH-CoV2 initiative - RNA binding domain of nucleocapsid phosphoprotein (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA binding domain of the nucleocapsid phosphoprotein in its APO form with Zn ions bound (PDB id:6VYO, Bioassembly 1). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The file 6VYO_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website. Additionally, the file 6VYO_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6VYO_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6VYO_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6VYO_SIRAHcg_prot.prmtop 6VYO_SIRAHcg_prot_10us_skip10ns.ncrst 6VYO_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (7.7 GB)
Represented Proteins: N protein
Represented Structures: 6VYO
Models: ---

SIRAH-CoV2 initiative - Nucleocapsid protein N-terminal RNA binding domain (10 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Nucleocapsid protein N-terminal RNA binding domain (PDB id:6M3M). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020.

The file 6M3M_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M3M_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M3M_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M3M_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd 6M3M_SIRAHcg_prot.prmtop 6M3M_SIRAHcg_prot_10us_skip10ns.ncrst 6M3M_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (4.2 GB)
Represented Proteins: N protein
Represented Structures: 6M3M
Models: ---



Simulations of Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an inhibitor-bound closed state (PDB entry 1R4L). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875754-structure.tar.gz

DESRES-Trajectory_sarscov2-10875754.mp4

Trajectory: Get Trajectory (852 MB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

HADDOCK docking of approved Drugbank set against human ACE2 ectodomain

P. I. Koukos, M. Réau, A. M. J. J Bonvin
Computational Structural Biology group, Bijvoet Centre for Biomolecular Research, Utrecht University
Repurposing study of the approved subset of Drugbank + active metabolites + investigational compounds of interest against human ACE2. Compounds are guided to the binding site using restraints extracted from PDB id 1r4l. The binding sire residues have been defined using a distance cut-off of 5Å. Docking is performed in vacuum using the OPLS (UA) forcefield with a shifting and switching function for vdW and electrostatics energies, respectively. Scaling of intermolecular energies was lowered to 1/1000 of their original values for the initial rigid-body docking stage to allow the compounds to more easily penetrate into the binding pocket. Compounds are scored using a scoring function comprised of the sum of vdW and electrostatics energies and an empirical desolvation potential.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingOtherN/AN/AvacuumN/AOPLS-UA
Input and Supporting Files:

README_ace2.pdf

Trajectory: Get Trajectory (23 GB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Docking-based repurposing study of approved drugs against truncated human ACE2 ectodomain (inhibitor-bound closed state)

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an apo open state (PDB entry 1R42). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875753-structure.tar.gz

DESRES-Trajectory_sarscov2-10875753.mp4

Trajectory: Get Trajectory (13 GB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2

DESRES-ANTON-10895671 30 µs of accelerated weighted ensemble MD simulation of a chimeric RBD in complex with ACE2 (30 µs )

D. E. Shaw Research
DESRES
SARS-CoV-2 attachment to host cells is mediated by a protein-protein interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike and the human ACE2 receptor. We performed a 30 µs of preliminary accelerated weighted ensemble (AWE) MD simulations of a chimeric RBD in complex with ACE2 (PDB entry 6VW1). In the simulation the complex was stable, and no dissociation events were observed. The AWE facilitated sampling of hundreds of binding and thousands of unbinding events over an aggregate 30 µs of AWE simulation. We provide all ~415,000 conformations sampled during the AWE simulations, and the corresponding graph adjacency matrix with weights. From analysis of the AWE simulation data, we also provide four representative trajectories containing binding events and a free energy landscape estimated using a history-augmented Markov state model. The complex model was solvated in a ~140 Å box of 200 mM NaCl and water, and parameterized with the DES-Amber protein and ion force field, the TIP4P-D water model, and an in-house force field derived from GAFF. Simulations were performed under the NPT ensemble at 300 K. During the AWE simulations, we used a 100.8 ps resampling interval to enhance the sampling of (i) the distance between the RBD and ACE2 centers of mass, (ii) the total number of atomic contacts between the RBD and ACE2, and (iii) the complex pRMSD (the square root of the product of the RMSD of the RBD after aligning on ACE2 and the RMSD of ACE2 after aligning on the RBD).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Weighted Ensemble Molecular DynamicsNPT3001water0.2DES-Amber
TIP4P-D
Modified GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10895671-bindingpaths.tar.gz

DESRES-Trajectory_sarscov2-10895671.mp4

Trajectory: Get Trajectory (48 GB)
Represented Proteins: RBD ACE2
Represented Structures: 6vw1
Models: Chimeric RBD in complex with human ACE2

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an inhibitor-bound closed state (PDB entry 1R4L). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875754-structure.tar.gz

DESRES-Trajectory_sarscov2-10875754.mp4

Trajectory: Get Trajectory (9.8 GB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein from a chimera construct of SARS-CoV-1 and SARS-CoV-2 (PDB entry 6VW1). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875775-structure.tar.gz

DESRES-Trajectory_sarscov2-10875775.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD
Represented Structures: 2ajf
Models: Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor in aqueous solution

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an apo open state (PDB entry 1R42). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875753-structure.tar.gz

DESRES-Trajectory_sarscov2-10875753.mp4

Trajectory: Get Trajectory (851 MB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein from a chimera construct of SARS-CoV-1 and SARS-CoV-2 (PDB entry 6VW1). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875775-structure.tar.gz

DESRES-Trajectory_sarscov2-10875775.mp4

Trajectory: Get Trajectory (21 GB)
Represented Proteins: ACE2 RBD
Represented Structures: 2ajf
Models: Chimeric RBD in complex with human ACE2

Inhibiting cleavage of the SARS-CoV-2 spike protein

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

Inhibition of formation of the viral fusion core

HADDOCK docking of approved Drugbank set against human ACE2 ectodomain

P. I. Koukos, M. Réau, A. M. J. J Bonvin
Computational Structural Biology group, Bijvoet Centre for Biomolecular Research, Utrecht University
Repurposing study of the approved subset of Drugbank + active metabolites + investigational compounds of interest against human ACE2. Compounds are guided to the binding site using restraints extracted from PDB id 1r4l. The binding sire residues have been defined using a distance cut-off of 5Å. Docking is performed in vacuum using the OPLS (UA) forcefield with a shifting and switching function for vdW and electrostatics energies, respectively. Scaling of intermolecular energies was lowered to 1/1000 of their original values for the initial rigid-body docking stage to allow the compounds to more easily penetrate into the binding pocket. Compounds are scored using a scoring function comprised of the sum of vdW and electrostatics energies and an empirical desolvation potential.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
DockingOtherN/AN/AvacuumN/AOPLS-UA
Input and Supporting Files:

README_ace2.pdf

Trajectory: Get Trajectory (23 GB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Docking-based repurposing study of approved drugs against truncated human ACE2 ectodomain (inhibitor-bound closed state)

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2 (725.3 µs )

Ivy Zhang
Folding@home -- Chodera lab

All-atom MD simulations of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to human angiotensin converting enzyme-related carboypeptidase (ACE2), simulated using Folding@Home. The “wild-type” RBD and three mutants (N439K, K417V, and the double mutant N439K/K417V) were simulated.

Complete details of this simulation are available here. Brief details appear below.

Preprint link will be posted shortly.

System preparation: The RBD:ACE2 complex was constructed from individual RBD (PDB: 6m0j, Chain E) and ACE2 (PDB: 1r42, Chain A) monomers aligned to the full RBD:ACE2 structure (PDB: 6m0j. These structural models were further refined by Tristan Croll using ISOLDE (Croll, 2018) and deposited in the Coronavirus Structural Taskforce (CST) database (Croll et al., 2020) to produce refined 6m0j and refined 1r42 models. The resulting RBD and ACE2 monomers were then aligned in PyMOL 2.3.2 to the CST 6m0j structure to create an initial RBD:ACE2 complex.

Full glycosylation patterns for ACE2 and RBD glycans were determined from Shajahan et al. For the constructed RBD:ACE2 complex, these included sites: N53, N90, N103, N322, N432, N546, and N690 on ACE2 and N343 on the RBD. Base NAG residues of each glycan structure (FA2, FA26G1, FA2, FA2, FA2G2, A2, FA2, FA2G2, respectively) were acquired from Elisa Fadda. Each glycan was then aligned to the corresponding NAG stub in the RBD:ACE2 model in and any resulting clashes were refined in ISOLDE. Full details of the glycosylation patterns / structures used and full workflow are available here.

Folding@home simulation: The equilibrated structure was then used to initiate parallel distributed MD simulations on Folding@home (Shirts and Pande, 2000, Zimmerman et al., 2020). Simulations were run with OpenMM 7.4.2 (Folding@home core22 0.0.13). Production simulations used the same Langevin integrator as the NpT equilibration described above. In total, 8000 independent MD simulations were generated on Folding@home. Conformational snapshots (frames) were stored at an interval of 0.5 ns/frame for subsequent analysis. The resulting final dataset contained 8000 trajectories, 725.3 us of aggregate simulation time, and 1450520 frames. Solute-only trajectories: The solute-only trajectories (with counterions) are available as MDTraj HDF5 files that contain both topology and trajectory information. A single trajectory of the WT RBD (RUN3) (~30 MB) can be downloaded using the AWS CLI:

aws s3 --no-sign-request cp s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311/run3-clone0.h5 .

All HDF5 trajectories (~300 GB) can be retrieved with

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/munged/solute/PROJ17311 .

Entire dataset: The raw Folding@home dataset is made available through the AWS Open Data Registry and can be retrieved through the AWS CLI. The dataset consists of a single project (PROJ17311) and has a RUN*/CLONE*/result* directory structure. RUNs denote different RBD mutants: N439K (RUN0), K417V (RUN1), N439K/K417V (RUN2), and WT (RUN3). CLONEs denote different independent replica trajectories.

To retrieve raw trajectory files in gromacs XTC format for the whole dataset (7 TB), you can use the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/raw-data/ .

Folding@home initial files: System setup and input files can be downloaded using the AWS CLI:

aws s3 --no-sign-request sync s3://fah-public-data-covid19-antibodies/vir-collaboration/SARS-CoV-2-ACE2-RBD/setup/ .

Contributors: Ivy Zhang, William G. Glass, Tristan I. Croll, Aoife M. Harbison, Elisa Fadda, John D. Chodera.

License: All data is freely available under the Creative Commons CC0 (“No Rights Reserved”) license.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15AMBER14SB
GLYCAM_06j-1
TIP3P
Input and Supporting Files: ---
Trajectory: Get Trajectory (2.1 TB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j 1R42
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2: ISOLDE refined model with N343 glycan Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE refined model with glycans

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an apo open state (PDB entry 1R42). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875753-structure.tar.gz

DESRES-Trajectory_sarscov2-10875753.mp4

Trajectory: Get Trajectory (13 GB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

Trajectory of the Spike protein in complex with human ACE2 (50 ns )

Oostenbrink Lab
University of Natural Resources and Life Sciences, Vienna
Atomistic MD simulations of the Spike protein in complex with the human ACE2 receptor, most probale glycosylations are added.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15GROMOS 54A8
GROMOS 53A6glyc
SPC
Input and Supporting Files:

inputdata.tar.gz

Trajectory: Get Trajectory (43 GB)
Represented Proteins: spike ACE2
Represented Structures: 6vyb 6m17
Models: Spike protein in complex with human ACE2

DESRES-ANTON-10895671 30 µs of accelerated weighted ensemble MD simulation of a chimeric RBD in complex with ACE2 (30 µs )

D. E. Shaw Research
DESRES
SARS-CoV-2 attachment to host cells is mediated by a protein-protein interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike and the human ACE2 receptor. We performed a 30 µs of preliminary accelerated weighted ensemble (AWE) MD simulations of a chimeric RBD in complex with ACE2 (PDB entry 6VW1). In the simulation the complex was stable, and no dissociation events were observed. The AWE facilitated sampling of hundreds of binding and thousands of unbinding events over an aggregate 30 µs of AWE simulation. We provide all ~415,000 conformations sampled during the AWE simulations, and the corresponding graph adjacency matrix with weights. From analysis of the AWE simulation data, we also provide four representative trajectories containing binding events and a free energy landscape estimated using a history-augmented Markov state model. The complex model was solvated in a ~140 Å box of 200 mM NaCl and water, and parameterized with the DES-Amber protein and ion force field, the TIP4P-D water model, and an in-house force field derived from GAFF. Simulations were performed under the NPT ensemble at 300 K. During the AWE simulations, we used a 100.8 ps resampling interval to enhance the sampling of (i) the distance between the RBD and ACE2 centers of mass, (ii) the total number of atomic contacts between the RBD and ACE2, and (iii) the complex pRMSD (the square root of the product of the RMSD of the RBD after aligning on ACE2 and the RMSD of ACE2 after aligning on the RBD).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Weighted Ensemble Molecular DynamicsNPT3001water0.2DES-Amber
TIP4P-D
Modified GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10895671-bindingpaths.tar.gz

DESRES-Trajectory_sarscov2-10895671.mp4

Trajectory: Get Trajectory (48 GB)
Represented Proteins: RBD ACE2
Represented Structures: 6vw1
Models: Chimeric RBD in complex with human ACE2

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2, no water or ions (2 µs )

D. E. Shaw Research
DESRES
78 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to the ectodomain of human ACE2 at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 78 putative ACE2 binding small molecules located at three regions on ACE2: a pocket underneath a helical bundle (residue 20-100; 51 molecules), a pocket involving a beta-hairpin structure (residue 346 to 360; 14 molecules) and a pocket behind a loop (residue 131-142; 13 molecules). The helical bundle and the beta-hairpin structure are known to interact with the RBD (receptor binding domain) of the spike protein and the loop structure is known to be involved in ACE2 homo-dimerization. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The ectodomain of human ACE2 is from PDB entry 6VW1. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10918441-set_ACE2-structure.tar.gz

DESRES-Trajectory_sarscov2-10918441-set_ACE2-table.csv

DESRES-Trajectory_sarscov2-10918441.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2
Represented Structures: 6vw1
Models:

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2 (2 µs )

D. E. Shaw Research
DESRES
78 2 µs trajectories of FDA approved or investigational drug molecules that in simulation remained bound to the ectodomain of human ACE2 at positions that might conceivably allosterically disrupt the interaction between these proteins. The small molecule drugs and their initial binding poses were chosen from a combination of molecular dynamics simulation and docking performed using an FDA-investigational drug library. The 78 putative ACE2 binding small molecules located at three regions on ACE2: a pocket underneath a helical bundle (residue 20-100; 51 molecules), a pocket involving a beta-hairpin structure (residue 346 to 360; 14 molecules) and a pocket behind a loop (residue 131-142; 13 molecules). The helical bundle and the beta-hairpin structure are known to interact with the RBD (receptor binding domain) of the spike protein and the loop structure is known to be involved in ACE2 homo-dimerization. The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for small molecules. The C- and N-peptide termini were capped with amide and acetyl groups respectively. The ectodomain of human ACE2 is from PDB entry 6VW1. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10918441-set_ACE2-structure.tar.gz

DESRES-Trajectory_sarscov2-10918441-set_ACE2-table.csv

DESRES-Trajectory_sarscov2-10918441.mp4

Trajectory: Get Trajectory (128 GB)
Represented Proteins: ACE2
Represented Structures: 6vw1
Models:

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an inhibitor-bound closed state (PDB entry 1R4L). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875754-structure.tar.gz

DESRES-Trajectory_sarscov2-10875754.mp4

Trajectory: Get Trajectory (9.8 GB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor (50 ns )

Negin Forouzesh, Alexey Onufriev
California State University, Los Angeles and Virginia Tech
50 ns simulation trajectory of a truncated SARS-CoV-2 spike receptor binding domain the human ACE2 receptor. The simulations used the Amber ff14SB force field and the OPC water model. The initial structure (PDB ID:6m0j) was truncated in order to obtain a smaller complex feasible with the computational framework. A molecular mechanics generalized Born surface area (MMGB/SA) approach was employed to estimate absolute binding free energy of the truncated complex. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M.The simulations were conducted at 300 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3000.987Water0.15FF14SB
Input and Supporting Files:

MD_Input

Trajectory: Get Trajectory (31 GB)
Represented Proteins: spike RBD ACE2
Represented Structures: 6m0j
Models: SARS-CoV-2 spike receptor-binding domain bound with ACE2

DESRES-ANTON-10857295 75 µs conventional MD simulation of a chimeric RBD in complex with ACE2, no water or ions (75 µs )

D. E. Shaw Research
DESRES
SARS-CoV-2 attachment to host cells is mediated by a protein-protein interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike and the human ACE2 receptor. We performed a 75 µs conventional MD simulation of a chimeric RBD in complex with ACE2 (PDB entry 6VW1). In the simulation the complex was stable, and no dissociation events were observed. We provide below the conventional MD simulation. The complex model was solvated in a ~140 Å box of 200 mM NaCl and water, and parameterized with the DES-Amber protein and ion force field, the TIP4P-D water model, and an in-house force field derived from GAFF. Simulations were performed under the NPT ensemble at 300 K. During the AWE simulations, we used a 100.8 ps resampling interval to enhance the sampling of (i) the distance between the RBD and ACE2 centers of mass, (ii) the total number of atomic contacts between the RBD and ACE2, and (iii) the complex pRMSD (the square root of the product of the RMSD of the RBD after aligning on ACE2 and the RMSD of ACE2 after aligning on the RBD).
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3001water0.2DES-Amber
TIP4P-D
Modified GAFF
Input and Supporting Files: ---
Trajectory: Get Trajectory (104 GB)
Represented Proteins: RBD ACE2
Represented Structures: 6vw1
Models: ---

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein from a chimera construct of SARS-CoV-1 and SARS-CoV-2 (PDB entry 6VW1). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875775-structure.tar.gz

DESRES-Trajectory_sarscov2-10875775.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD
Represented Structures: 2ajf
Models: Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor in aqueous solution

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an apo open state (PDB entry 1R42). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875753-structure.tar.gz

DESRES-Trajectory_sarscov2-10875753.mp4

Trajectory: Get Trajectory (851 MB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein from a chimera construct of SARS-CoV-1 and SARS-CoV-2 (PDB entry 6VW1). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875775-structure.tar.gz

DESRES-Trajectory_sarscov2-10875775.mp4

Trajectory: Get Trajectory (21 GB)
Represented Proteins: ACE2 RBD
Represented Structures: 2ajf
Models: Chimeric RBD in complex with human ACE2

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated in an inhibitor-bound closed state (PDB entry 1R4L). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10875754-structure.tar.gz

DESRES-Trajectory_sarscov2-10875754.mp4

Trajectory: Get Trajectory (852 MB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)


Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

Inhibiting cleavage of the SARS-CoV-2 spike protein

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

Inhibition of formation of the viral fusion core

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex (4 µs )

Florencia Klein
Institut Pasteur de Montevideo -- Biomolecular Simulations Laboratory

This dataset contains an trajectory of four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at SIRAH website.

Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar

2- Open the trajectory on VMD using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot_4us_skip10ns.ncrst 6M17_SIRAHcg_prot_4us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.

TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Coarse Grained Molecular DynamicsNPT3001water0.15SIRAH 2.2
Input and Supporting Files: ---
Trajectory: Get Trajectory (20.1 GB)
Represented Proteins: spike RBD ACE2 BoAT1
Represented Structures: 6M17
Models: ---

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions (10 µs )

D. E. Shaw Research
DESRES
10 µs simulation trajectory of the human ACE2 ectodomain was initiated from ACE2 in complex with with the receptor binding domain of spike protein SARS-COV-2 (PDB entry 6M17). The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.
TypeEnsembleTemperature (K)Pressure (atm)SolventSalinity (M)Force Fields
Molecular DynamicsNPT3101water0.15Amber99sb-ildn
TIP3P
GAFF
Input and Supporting Files:

DESRES-Trajectory_sarscov2-10905033-structure.tar.gz

DESRES-Trajectory_sarscov2-10905033.mp4

Trajectory: Get Trajectory (1.1 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution


Ab Receptor in Host Cells (FcR)


Furin / PACE


Interleukin-6 (IL-6) receptor


Programmed cell death factor 1


p38 Mitogen-Activated Protein Kinase (MPAK)


Transmembrane Protease Serine 2