Dynamic Structural models

Proteins from the SARS-CoV-2 Proteome

The data in this page includes models, simulation trajectories, and results from docking screens.  It is being made available for commercial and non-commercial use provided it is accompanied by an appropriate citation to this site and the following preprint:  Smith MD and Smith JC, Repurposing therapeutics for COVID-19: Supercomputer-based docking to the viral spike protein and viral spike protein-human ACE2 interface. ChemRxiv, 2020.

Data under models contains a representative set of protein conformations gathered from C-alpha clustering of our enhanced-sampling trajectories gathered at 310 K.  Data under SImulations contains snapshots of the 310K trajectories taken every 1 nanosecond.  Data under docking contains docked ligand configurations and scores from our drug repurposing database screens to each conformer.

Spike glycoprotein RBD (X-ray)

S-protein simulated from a recent X-ray crystal structure of the S protein RBD.

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Spike:ACE2 complex (homology)

Early model of SARS-CoV-2 S protein RBD (homology model) bound to human ACE2

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-Please contact Micholas Smith for access to the docking results.

Spike glycoprotein RBD (homology model)

SARS-CoV-2 S-protein RBD (homology model)

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

NSP9 dimer

SARS-CoV-2 Nsp9 RNA binding protein (dimer)

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

NSP3 phosphatase domain

X-ray crystal structure of ADP ribose phosphatase domain of NSP3 from SARS CoV-2 in complex with ADP ribose

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

NSP10: NSP16 complex

SARS-CoV-2 NSP10:NSP16 complex

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Main protease monomer

X-ray crystal structure of the SARS-CoV-2 main protease (monomer)

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Main protease dimer

X-ray crystal structure of the SARS-CoV-2 main protease (dimer)

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Endoribonuclease (tagged monomer)

SARS-CoV-2 NSP15 endoribonuclease (monomer). Includes a non-native three-residue N-terminal tag affinity purification tag.

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Endoribonuclease (tagged hexamer)

SARS-CoV-2 NSP15 endoribonuclease (hexamer), Includes a non-native
three-residue N-terminal affinity purification tag.

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Endoribonuclease monomer

SARS-CoV-2 NSP15 endoribonuclease (monomer). This is the biological sequence, which differs slightly from the sequence in the PDB file.

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

Endoribonuclease biological complex

SARS-CoV-2 NSP15 endoribonuclease (hexamer). This is the biological sequence, which differs slightly from the sequence in the PDB file.

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.

NSP16

SARS-CoV-2 NSP16 extracted from an X-ray crystal structure of NSP16-NSP10 complex (6W4H).

*Coming Soon*

 

-Please contact Micholas Smith for access to the docking results.