Contributions by the Biomolecular Simulations Laboratory Organization

Biomolecular Simulations Laboratory's Simulations

SIRAH-CoV2 initiative - Apo ADP-ribose phosphatase of NSP3

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex

SIRAH-CoV2 initiative - NSP7-NSP8 complex

SIRAH-CoV2 initiative - Co-factor complex of NSP7 and the C-terminal domain of NSP8

SIRAH-CoV2 initiative - Glycosylated RBD

SIRAH-CoV2 initiative - Helicase

SIRAH-CoV2 initiative - Membrane embedded ORF3a

SIRAH-CoV2 initiative - NSP9 RNA binding protein

SIRAH-CoV2 initiative - Nucleocapsid protein N-terminal RNA binding domain

SIRAH-CoV2 initiative - ORF7A enconded accessory protein

SIRAH-CoV2 initiative - Papain-like Protease

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481

SIRAH-CoV2 initiative - RNA binding domain of nucleocapsid phosphoprotein

SIRAH-CoV2 initiative - RNA-dependent RNA polymerase in complex with cofactors NSP7 and NSP8

SIRAH-CoV2 initiative - S1 Receptor Binding Domain in complex with human antibody CR3022

SIRAH-CoV2 initiative - S2 Spike core fragment in postfusion state

SIRAH-CoV2 initiative - Spike´s RBD/ACE2-B0AT1 complex

SIRAH-CoV2 initiative - Main Protease

SIRAH-CoV2 initiative - NSP15 Endonuclease

Contributions by the D. E. Shaw Research Organization

D. E. Shaw Research's Models

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

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

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

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

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

Human ACE2 ectodomain in aqueous solution (apo open state)

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

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

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

Chimeric RBD in complex with human ACE2

Chimeric RBD in complex with human ACE2

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

D. E. Shaw Research's Simulations

DESRES-ANTON-10857295 75 µs conventional MD simulation of a chimeric RBD in complex with ACE2, no water or ions

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

DESRES-ANTON-10875753 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

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

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution

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

DESRES-ANTON-10895671 30 µs of accelerated weighted ensemble MD simulation of a chimeric RBD in complex with ACE2

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

DESRES-ANTON-10897136 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-10897850 10 µs simulation of of the trimeric SARS-CoV-2 spike glycoprotein, no water or ions

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

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

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

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

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2, no water or ions

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

DESRES-ANTON-11021566 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

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

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

DESRES 100 µs MD of 3CLpro, All Atom

Contributions by the Folding @ Home Organization

Folding @ Home's Models

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

Folding @ Home's Simulations

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

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

Folding@home simulations of the SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2

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

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

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S309

Folding@home simulations of the SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309

Folding@home simulations of the SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309

Folding@home simulations of the apo SARS-CoV-2 spike RBD (with glycosylation)

Folding@home simulations of the apo SARS-CoV-2 spike RBD (without glycosylation)

Folding@home simulations of nsp10

Folding@home simulations of nsp12

Folding@home simulations of nsp13

Folding@home simulations of nsp3 macrodomain

Folding@home simulations of nsp3 pl2pro domain

Folding@home simulations of nsp5 dimer

Folding@home simulations of nsp5 monomer

Folding@home simulations of nsp7

Folding@home simulations of nsp8

Folding@home simulations of nsp9

Folding@home simulations of the SARS-CoV-2 spike protein

Contributions by the Tri-Institutional Therapeutics Discovery Institute Organization

Tri-Institutional Therapeutics Discovery Institute's Models

TMPRSS2 Homology Model With Benzamidine Overlaid

TMPRSS2 Homology Model With Substrate Overlaid