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 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

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: [.] [.]
Trajectory: Get Trajectory (62 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, 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: [.] [.]
Trajectory: Get Trajectory (5.3 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open 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: [.] [.]
Trajectory: Get Trajectory (51 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: Improved trimeric SARS-CoV-2 spike glycoprotein (closed 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: [.] [.]
Trajectory: Get Trajectory (67 GB)
Represented Proteins: spike
Represented Structures: 6vyb
Models: Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

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

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: [.] [.]
Trajectory: Get Trajectory (49 GB)
Represented Proteins: spike
Represented Structures: 6vxx
Models: 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, 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: [.] [.]
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-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: [.] [.] [.]
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

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: [.] [.] [.]
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

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

No Targets Recorded

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:

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:

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:

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: [.]
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


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, 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

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: [.]
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

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

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

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


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


SARS-CoV-2 RNA Polymerase (NSP12)

Inhibition of viral polymerases

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: [.] [.]
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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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


Helicase coronavirus nonstructural protein 13 (NSP13)


Coronavirus nonstructural protein 1


Coronavirus nonstructural protein 10


Coronavirus nonstructural protein 11


Coronavirus nonstructural protein 14


Coronavirus nonstructural protein 15


Coronavirus nonstructural protein 16


Coronavirus nonstructural protein 2


Coronavirus nonstructural protein 4


Coronavirus nonstructural protein 6


Coronavirus nonstructural protein 7

Inhibition of viral polymerases

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: [.] [.]
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 + 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: [.] [.]
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, 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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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

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: [.] [.]
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 + 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: [.] [.]
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

No Targets Recorded


Coronavirus nonstructural protein 9


Simulations of Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10


Coronavirus Open Reading Frame 3a


Coronavirus Open Reading Frame 6


Coronavirus Open Reading Frame 7a


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



Simulations of Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

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

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: [.] [.]
Trajectory: Get Trajectory (851 MB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

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: [.] [.]
Trajectory: Get Trajectory (13 GB)
Represented Proteins: ACE2
Represented Structures: 1r42
Models: Human ACE2 ectodomain in aqueous solution (apo open state)

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: [.] [.]
Trajectory: Get Trajectory (9.8 GB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

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: [.] [.]
Trajectory: Get Trajectory (852 MB)
Represented Proteins: ACE2
Represented Structures: 1r4l
Models: Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

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: [.] [.]
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, 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: [.] [.]
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

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: [.] [.]
Trajectory: Get Trajectory (21 GB)
Represented Proteins: ACE2 RBD
Represented Structures: 2ajf
Models: Chimeric RBD 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: [.] [.]
Trajectory: Get Trajectory (48 GB)
Represented Proteins: RBD ACE2
Represented Structures: 6vw1
Models: Chimeric RBD in complex with human ACE2

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: [.] [.]
Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2 RBD BoAT1
Represented Structures: 6m17
Models: SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

No Targets Recorded

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: [.] [.] [.]
Trajectory: Get Trajectory (128 GB)
Represented Proteins: ACE2
Represented Structures: 6vw1
Models:

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: ---

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: [.] [.] [.]
Trajectory: Get Trajectory (14 GB)
Represented Proteins: ACE2
Represented Structures: 6vw1
Models:


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, 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: [.] [.]
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

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: [.] [.]
Trajectory: Get Trajectory (14 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