Models

Structural models for use in virtual screening, free energy calculations, and molecular simulation.

Many models come from the Coronavirus Structural Task Force.

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

Quick Navigation

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

Models of Virion Particle

Coarse Grained SARS-CoV-2 Virion

Alvin Yu, Gregory A. Voth
University of Chicago -- Voth Lab
Represented Proteins: virion
Model: Files | Source Structure PDBs: ---
A coarse-grained (CG) model for the SARS-CoV-2 virion (in its entirety) developed under an NSF RAPID award 2029092 to G.A.V. in response to the COVID-19 pandemic.
Simulations:

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Models 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

Trimeric SARS-CoV-2 spike glycoprotein (open state) in aqueous solution

DESRES
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6VYB | Visualize: 3DMol.js
Solvated structure of the trimeric SARS-CoV-2 spike glycoprotein in open state. 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 solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 715439.
Simulations:

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

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

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

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


spike_full-length_closed_amarolab

Amaro Lab
University of California San Diego
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6VXX
PSF/PDB for full-length SPIKE protein in the Closed state, including protein, glycans, membrane, water and ions.
Simulations:

Trajectories of full-length SPIKE protein in the Closed state.


Trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

DESRES
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6VXX | Visualize: 3DMol.js
Solvated structure of the trimeric SARS-CoV-2 spike glycoprotein in closed state. 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 solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M. The total number of atoms in the system was 566502.
Simulations:

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

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


SARS-CoV-2 trimeric spike protein binding to FDA approved or investigational drug molecules

DESRES
Represented Proteins: spike RBD
Model: Files | Source Structure PDBs: 6VXX 6VW1 | Visualize: 3DMol.js
Spike trimer constructed 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.
Simulations:

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

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


Improved trimeric SARS-CoV-2 spike glycoprotein (closed state) in aqueous solution

DESRES
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6VXX | Visualize: 3DMol.js
Solvated structure of the trimeric SARS-CoV-2 spike glycoprotein in closed state. The C- and N-peptide termini are capped with amide and acetyl groups respectively. The system was solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M.
Simulations:

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

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


No Targets Recorded

spike_full-length_open_amarolab

Amaro Lab
University of California San Diego
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6VSB
PSF/PDB for full-length SPIKE protein in the Open state, including protein, glycans, membrane, water and ions.
Simulations:

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

Trajectories of full-length SPIKE protein in the Open state.


SARS-CoV-2 spike protein trimer (closed state) model for MD simulations

Vladimir Mironov
Lomonosov Moscow State University -- Chemistry Department -- Laboratory of Chemical Cybernetics
Represented Proteins: spike
Model: Files | Source Structure PDBs: 6ACK | Visualize: 3DMol.js
Model of the spike protein trimer of SARS-CoV-2 virus in closed conformation. That trimer is built from the homology model of monomer made by Thomas Desautels et.al. (https://doi.org/10.1101/2020.04.03.024885) It has been replicated and fitted to the known structure of SARS-CoV-1 by Wenfei Song et.al. PDBID: 6ACK (https://doi.org/10.1371/journal.ppat.1007236). That model has been made to perform MD simulations.
Simulations:

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


SWISS-MODEL Spike + ACE2

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: spike ACE2
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


SWISS-MODEL Spike

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: spike
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


spike by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: spike
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

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Models of Viral Protease, Polymerase, and Nonstructured Proteins

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

3CLpro / Mpro activity

3CLpro prepared for simulation in a 120 cubic A box for long continuous trajectory

DESRES
Represented Proteins: 3CLpro
Model: Files | Source Structure PDBs: 6Y84
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.
Simulations:

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

DESRES 100 µs MD of 3CLpro, All Atom


SARS-CoV-2 dimeric main protease without ligand based on PDB 6LU7

Teruhisa S. Komatsu, Yohei M. Koyama, Noriaki Okimoto, Gentaro Morimoto, Yousuke Ohno, Makoto Taiji
Riken Biosystems Dynamics Research
Represented Proteins: 3CLpro
Model: Files | Source Structure PDBs: 6LU7
Simulations:

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 200ps

Riken BDR 10 Microsecond Trajectory System Snapshot every 10ns

Riken BDR 10 Microsecond Trajectory Protein Snapshot every 1ns


No Targets Recorded

SWISS-MODEL 3CLpro

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: 3CLpro
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


3CLpro by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: 3CLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



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

Inhibition of PLpro protease activity

SARS-CoV-2 PLpro: ISOLDE refined model

Tristan Croll
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: 6W9C | Visualize: 3DMol.js
Refinement of 6w9c (a 2.7A X-ray structure) of papain-like protease of SARS-CoV-2 that contains three copies of the same chain in the asymmetric unit. Corrects several issues: * Corrects zinc site in chain A misidentified as a disulfide, and incompletely modeled site in chain B; the same zinc site is correctly modeled in chain C. * Cleans up lots of issues due to missing data (overall completeness 57.1%) See a complete description of the issues remedied by this model.
Simulations:

---


No Targets Recorded

Refinement of SWISS-MODEL PL-Pro domain 4 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


SWISS-MODEL PL-PRO

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


Refinement of SWISS-MODEL PL-Pro domain 2 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of SWISS-MODEL PL-Pro domain 7 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX PLpro by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of AplhaFold PLpro C terminal by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of PLpro by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


PLpro by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


Refinement of SWISS-MODEL PL-Pro domain 5 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: PLpro
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

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SARS-CoV-2 RNA Polymerase (NSP12)

Inhibition of viral polymerases

SARS-CoV-2 RdRP (NSP12) in complex with NSP7 and two copies of NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
Refinement of 6m71 that fixes multiple issues: * Corrects incorrect modeling of both zinc binding sites (originally modeled as disulfides) * Corrects 1-2 dozen rotamer adjustments and peptide flips * Models C-terminal domain of chain D (one of the NSP8s) using well-resolved chain B See a complete description of the issues remedied by this model.
Simulations:

---


SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

DESRES
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
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.
Simulations:

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

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


SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BTF 7BV1 | Visualize: 3DMol.js
Model of the apo-protein form of RdRp complex of the SARS-CoV-2 is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71,7BV1) kindly shared with us by Gao et.al. The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BV2 | Visualize: 3DMol.js
Model of the RdRp + RNA + NTP complex of the SARS-CoV-2 with non-covalently bound NTP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and Remdesivir molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.5 Å) with the recently published RdRp complex with RNA template-primer and covalently bound Remdesivir in mono-phosphate form (PDB:7BV2, 6YYT) The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 7BTF 7BV2 6YYT | Visualize: 3DMol.js
Model of the RdRp + RNA + ATP complex of the SARS-CoV-2 with non-covalently bound ATP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and ATP molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.7 Å) with the recently published RdRp complex with RNA template-primer (PDB:7BV2, 6YYT). The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


No Targets Recorded

SWISS-MODEL NSP7 + NSP8 + RdRP

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP7 NSP8 RdRP
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


RdRP by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: RdRP
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SARS-CoV RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR | Visualize: 3DMol.js
Refinement of 6nur that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

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SARS-CoV-2 RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 7BTF | Visualize: 3DMol.js
Refinement of 7btf that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

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Helicase coronavirus nonstructural protein 13 (NSP13)

No Targets Recorded

SWISS-MODEL Helicase

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: Helicase
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


Helicase (NSP13) by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: Helicase
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus nonstructural protein 1

No Targets Recorded

Refinement of nsp1 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP1
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of SWISS-MODEL nsp1 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP1
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


NSP1 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP1
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus nonstructural protein 10

No Targets Recorded

SWISS-MODEL NSP10

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP10
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


NSP10 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP10
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SWISS-MODEL NSP10 + NSP14

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP10 NSP14
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


SWISS-MODEL NSP10 + NSP16

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP10 NSP16
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Coronavirus nonstructural protein 11


Coronavirus nonstructural protein 14

No Targets Recorded

NSP14 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP14
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SWISS-MODEL NSP10 + NSP14

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP10 NSP14
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Coronavirus nonstructural protein 15

No Targets Recorded

SWISS-MODEL NSP15

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP15
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


NSP15 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP15
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus nonstructural protein 16

No Targets Recorded

NSP16 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP16
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SWISS-MODEL NSP10 + NSP16

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP10 NSP16
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Coronavirus nonstructural protein 2

No Targets Recorded

Refinement of nsp2 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX nsp2 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


NSP2 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


Refinement of Baker nsp2 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of Baker lab’s models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of AplhaFold nsp2 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---



Coronavirus nonstructural protein 4

No Targets Recorded

SWISS-MODEL NSP4

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


Refinement of RaptorX nsp4 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of AplhaFold nsp4 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of NSP4 in membrane environment by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Model re-built with additional information. Refined with consideration of membrane environment. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of SWISS-MODEL NSP4 domain 3 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


NSP4 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


Refinement of nsp4 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP4
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---



Coronavirus nonstructural protein 6

No Targets Recorded

NSP6 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


Refinement of RaptorX nsp6 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of NSP6 in membrane environment by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Used the AlphaFold model, refined with consideration of membrane environment. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of AplhaFold nsp6 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of nsp6 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: NSP6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---



Coronavirus nonstructural protein 7

Inhibition of viral polymerases

SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

DESRES
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
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.
Simulations:

DESRES-ANTON-10917618 10 µs simulation of 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


SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BTF 7BV1 | Visualize: 3DMol.js
Model of the apo-protein form of RdRp complex of the SARS-CoV-2 is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71,7BV1) kindly shared with us by Gao et.al. The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BV2 | Visualize: 3DMol.js
Model of the RdRp + RNA + NTP complex of the SARS-CoV-2 with non-covalently bound NTP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and Remdesivir molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.5 Å) with the recently published RdRp complex with RNA template-primer and covalently bound Remdesivir in mono-phosphate form (PDB:7BV2, 6YYT) The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 7BTF 7BV2 6YYT | Visualize: 3DMol.js
Model of the RdRp + RNA + ATP complex of the SARS-CoV-2 with non-covalently bound ATP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and ATP molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.7 Å) with the recently published RdRp complex with RNA template-primer (PDB:7BV2, 6YYT). The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRP (NSP12) in complex with NSP7 and two copies of NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
Refinement of 6m71 that fixes multiple issues: * Corrects incorrect modeling of both zinc binding sites (originally modeled as disulfides) * Corrects 1-2 dozen rotamer adjustments and peptide flips * Models C-terminal domain of chain D (one of the NSP8s) using well-resolved chain B See a complete description of the issues remedied by this model.
Simulations:

---


No Targets Recorded

SARS-CoV-2 RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 7BTF | Visualize: 3DMol.js
Refinement of 7btf that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

---


SWISS-MODEL NSP7 + NSP8 + RdRP

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP7 NSP8 RdRP
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


SWISS-MODEL NSP7 + NSP8

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP7 NSP8
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


SARS-CoV RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR | Visualize: 3DMol.js
Refinement of 6nur that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

---


NSP7 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP7
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus nonstructural protein 8

Inhibition of viral polymerases

SARS-CoV-2 RdRP (NSP12) in complex with NSP7 and two copies of NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
Refinement of 6m71 that fixes multiple issues: * Corrects incorrect modeling of both zinc binding sites (originally modeled as disulfides) * Corrects 1-2 dozen rotamer adjustments and peptide flips * Models C-terminal domain of chain D (one of the NSP8s) using well-resolved chain B See a complete description of the issues remedied by this model.
Simulations:

---


SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

DESRES
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6M71 | Visualize: 3DMol.js
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.
Simulations:

DESRES-ANTON-10917618 10 µs simulation of 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


SARS-CoV-2 apo-RdRp complex (nsp12+2*nsp8+nsp7) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BTF 7BV1 | Visualize: 3DMol.js
Model of the apo-protein form of RdRp complex of the SARS-CoV-2 is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71,7BV1) kindly shared with us by Gao et.al. The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + RTP (Remdesivir Tri-phosphate) model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 6M71 7BV2 | Visualize: 3DMol.js
Model of the RdRp + RNA + NTP complex of the SARS-CoV-2 with non-covalently bound NTP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and Remdesivir molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.5 Å) with the recently published RdRp complex with RNA template-primer and covalently bound Remdesivir in mono-phosphate form (PDB:7BV2, 6YYT) The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


SARS-CoV-2 RdRp complex (nsp12+2*nsp8+nsp7) + RNA template-primer + ATP model for MD simulations

Vaibhav Modi
University of Jyväskylä -- Department of Chemistry and Nanoscience Center -- Computational Biomolecular Chemistry Group
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR 7BTF 7BV2 6YYT | Visualize: 3DMol.js
Model of the RdRp + RNA + ATP complex of the SARS-CoV-2 with non-covalently bound ATP molecule is built using homology modelling with the SARS-CoV-1 RdRp complex (PDB:6NUR) as template structure (https://doi.org/10.1038/s41467-019-10280-3). The modelled structure shows excellent fit (< 0.6 Å) to the SARS-CoV-2 RdRp complex (PDB:6M71) kindly shared with us by Gao et.al. Further, the model of RdRp complex with RNA and ATP molecule in Tri-phosphate form is modelled based on comparative fitting with previously known poliovirus and norovirus structres (with NTP molecule in hydrophobic cleft). The protein-RNA complex with Remdesivir shows excellent fit (< 0.7 Å) with the recently published RdRp complex with RNA template-primer (PDB:7BV2, 6YYT). The fitted models have been equilibriated to perform long MD simulations.
Simulations:

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


No Targets Recorded

SWISS-MODEL NSP7 + NSP8

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP7 NSP8
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


NSP8 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP8
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SARS-CoV RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 6NUR | Visualize: 3DMol.js
Refinement of 6nur that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

---


SARS-CoV-2 RdRP (NSP12) in complex with cofactors NSP7 and NSP8: ISOLDE refined model

Tristan Croll
Represented Proteins: RdRP NSP7 NSP8
Model: Files | Source Structure PDBs: 7BTF | Visualize: 3DMol.js
Refinement of 7btf that fixes misthreading in the vininity of residues 910-920 where residues were shifted within density by 9 residues. See a complete description of the issues remedied by this model.
Simulations:

---


SWISS-MODEL NSP7 + NSP8 + RdRP

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP7 NSP8 RdRP
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Coronavirus nonstructural protein 9

No Targets Recorded

NSP9 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: NSP9
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SWISS-MODEL NSP9

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: NSP9
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Models of Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10

No Targets Recorded

Refinement of RaptorX ORF10 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF10
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of ORF10 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF10
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


ORF10 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: ORF10
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus Open Reading Frame 3a

No Targets Recorded

Refinement of ORF3a by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF3a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX ORF3a by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF3a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of AplhaFold ORF3a by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF3a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


ORF3a by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: ORF3a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus Open Reading Frame 6

No Targets Recorded

Refinement of ORF6 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX ORF6 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


ORF6 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: ORF6
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus Open Reading Frame 7a

No Targets Recorded

Refinement of ORF7a by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF7a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


SWISS-MODEL Protein 7a

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: ORF7a
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---


Refinement of SWISS-MODEL ORF7a by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF7a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


ORF7a by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: ORF7a
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Coronavirus Open Reading Frame 7b

No Targets Recorded

Refinement of ORF7b by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF7b
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX ORF7b by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF7b
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---



Coronavirus Open Reading Frame 8

No Targets Recorded

Refinement of RaptorX ORF8 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF8
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of ORF8 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF8
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


ORF8 by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: ORF8
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


Refinement of SWISS-MODEL ORF8 by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: ORF8
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of SWISS-MODEL models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---



Models of Viral Membrane Proteins

Membrane Glycoprotein

No Targets Recorded

Refinement of AplhaFold M_protein by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: M protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Physics-based refinement of Google DeepMind AlphaFold models from early March 2020. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of RaptorX M_protein by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: M protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
FeigLab refinement of RaptorX-Contact models. Refinement performed using a protocol based on molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of M_protein by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: M protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Contact-based structure prediction using trRosetta. 10 models generated and the best scoring was refined through molecular dynamics (MD) simulations. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


Refinement of M Protein in membrane environment by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: M protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Monomer structure revised using FeigLab and AlphaFold models. Refined with consideration of membrane environment. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


M protein by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: M protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Models of Viral Envelope Proteins

Envelope small membrane protein

No Targets Recorded

Refinement of E protein in membrane environment by FeigLab

Feig Computational Biophysics Lab
Michigan State University
Represented Proteins: E protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
Monomer structure produced using FeigLab pipeline. Refined with consideration of membrane environment. See https://github.com/feiglab/sars-cov-2-proteins for a complete description of the process.
Simulations:

---


E protein by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: E protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---



Models of Viral Nucleocapsid Proteins

Nucleoprotein

No Targets Recorded

N protein by Yang Zhang lab

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang
Depeartment of Computational Medicine and Bioinformatics -- University of Michigan -- Yang Zhang
Represented Proteins: N protein
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
model from deep learning contact-map assisted C-I-TASSER structure simulation
Simulations:

---


SWISS-MODEL N Protein

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: N protein
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Models of Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

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

Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor in aqueous solution

DESRES
Represented Proteins: ACE2 RBD
Model: Files | Source Structure PDBs: 2AJF | Visualize: 3DMol.js
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 solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns.
Simulations:

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex, no water or ions


Human ACE2 ectodomain in aqueous solution (apo open state)

DESRES
Represented Proteins: ACE2
Model: Files | Source Structure PDBs: 1R42 | Visualize: 3DMol.js
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.
Simulations:

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions

DESRES-ANTON-10875753 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution


Human ACE2 ectodomain in aqueous solution (inhibitor-bound closed state)

DESRES
Represented Proteins: ACE2
Model: Files | Source Structure PDBs: 1R4L | Visualize: 3DMol.js
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.
Simulations:

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain, no water or ions

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution


Chimeric RBD in complex with human ACE2

DESRES
Represented Proteins: ACE2 RBD
Model: Files | Source Structure PDBs: 6VW1 | Visualize: 3DMol.js
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:

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SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

DESRES
Represented Proteins: ACE2 RBD BoAT1
Model: Files | Source Structure PDBs: 6M17 | Visualize: 3DMol.js
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 solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns.
Simulations:

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution


Chimeric RBD in complex with human ACE2

DESRES
Represented Proteins: ACE2 RBD
Model: Files | Source Structure PDBs: 6VW1 | Visualize: 3DMol.js
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:

---


No Targets Recorded

SWISS-MODEL Spike + ACE2

SWISS-MODEL team, Schwede Group
Swiss Institute of Bioinformatics, Biozentrum, University of Basel
Represented Proteins: spike ACE2
Model: Files | Source Structure PDBs: ---
Full SARS-CoV-2 proteome modeled. Follow the Model link for weekly updated models and PDB structures. All models include global and per-residue quality estimates.
Simulations:

---



Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

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

SARS-CoV-2 RBD/ACE2-B0AT1 complex in aqueous solution

DESRES
Represented Proteins: ACE2 RBD BoAT1
Model: Files | Source Structure PDBs: 6M17 | Visualize: 3DMol.js
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 solvated, neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns.
Simulations:

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex, no water or ions

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 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

No Targets Recorded

TMPRSS2 Homology Model With Benzamidine Overlaid

David Huggins
Tri-Institutional Therapeutics Discovery Institute
Represented Proteins: TMPRSS2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
TMPRSS2 homology model based on the structure of TMPRSS15/Enteropeptidase from PDBID 4DGJ with Benzamidine Overlaid
Simulations:

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TMPRSS2 Homology Model With Substrate Overlaid

David Huggins
Tri-Institutional Therapeutics Discovery Institute
Represented Proteins: TMPRSS2
Model: Files | Source Structure PDBs: --- | Visualize: 3DMol.js
TMPRSS2 homology model based on the structure of TMPRSS15/Enteropeptidase from PDBID 4DGJ with SARS-CoV-2 substrate peptide overlaid
Simulations:

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External Model Resources

Structure Models of All Mature Peptides in 2019-NCoV Genome by C-I-TASSER

Description: This page contains 3D structural models and function annotation for all proteins encoded by the genome of 2019-nCoV, also known as SARS-CoV-2, which is the novel coronavirus causing the COVID-19 pneumonia. The structure models are generated by the C-I-TASSER pipeline, which utilizes deep convolutional neural-network based contact-map predictions to guide the I-TASSER fragment assembly simulations. Benchmark and blind CASP tests showed that C-I-TASSER generates models with a higher accuracy than I-TASSER does, especially for the protein targets lack of homologous templates. For multi-domain targets, the C-I-TASSER structure of individual domains are assembled by DEMO into full length structure.

Institution: University of Michigan

Lab: Yang Zhang


Tristan Croll ISOLDE COVID-19 Models

Description: Models refined by Tristan Croll in ISOLDE

Institution: Cambridge Institute for Medical Research


Solvation Maps for COVID19-Related Protein Targets

Description: This is a free online repository for sharing GIST/HSA data of COVID19 related protein targets. Currently, we have th3 GIST/HSA data for 7 targets (6LU7, 6YB7, 6M03, 6Y84, 6W63, 6JYT and 6W4H).

Institution: Lehman College, City University of New York

Lab: Tom Kurtzman


PubChem

Description: PubChem is a public chemistry database at the National Institutes of Health (NIH). Since the launch in 2004, PubChem has become a key chemical information resource for scientists, students, and the general public. Each month our website and programmatic services provide data to several million users worldwide. PubChem mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. We collect information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.

Institution: NIH


Structural Biology Task Force GitHub Page

Description: A global public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2.

Organization: Coronavirus Structural Biology Task Force