Molecular Dynamics Simulations Related to SARS-CoV-2

D. E. Shaw Research has released trajectories from molecular dynamics simulations related to our study of SARS-CoV-2, along with videos that visualize the trajectories. Our scientists obtained this data by running long simulations on our Anton supercomputers.1 In most cases, these trajectories and associated preliminary observations have not been peer reviewed or experimentally verified, and their accuracy is thus uncertain.

We are providing these simulation trajectories and videos to the scientific community under the Creative Commons Attribution 4.0 International Public License in the hopes that their release might be helpful to other scientists working to understand SARS-CoV-2 and to develop therapies for COVID-19.

If you have questions or comments about the simulations, please contact us. Follow us on Twitter for updates.

The use of this simulation data in any published work should be acknowledged by including a citation to: D. E. Shaw Research, "Molecular Dynamics Simulations Related to SARS-CoV-2," D. E. Shaw Research Technical Data, 2020. https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/

I have read and agree to the terms and conditions of the Creative Commons Attribution 4.0 International Public License.



   
   

DESRES-ANTON-[15235444, 15235449, 15235455, 15256595, 15256598, 15256602]

Release date: June 22nd, 2022

  • Here, we present sequences for peptides we designed to modulate SARS-CoV-2 RdRp activity by binding to the NiRAN domain, as well as in silico, in vitro, and cellular data on their activity.
    • D. E. Shaw Research
   
   

DESRES-ANTON-13795965

Release date: November 14th, 2021

  • A 500-µs trajectory featuring nsp13-bound SARS-CoV-2 replication-transcription complex, starting from the nsp13.1-open conformation with three cytosines (chain P and residues 36, 37, and 38) manually built onto the 3' end of chain P, extending the product RNA into the NTP-entry channel of nsp12 to mimic the backtracked state of nsp12.
   
   

DESRES-ANTON-12212688

Release date: November 13th, 2021

  • A 20 µs simulation of nsp13 bound to ADPMg2+ starting from the nsp13.1-open conformation.
   
   

DESRES-ANTON-12366060

Release date: March 16th, 2021

  • A 5 µs simulation of the nsp13-bound SARS-CoV-2 replication-transcription complex starting from a backtracked state featuring p-RNA with a matched -1U and a mismatched +1C.
   
   

DESRES-ANTON-11441075

Release date: July 15th, 2020

  • A 100 µs simulation of the apo papain-like protease of SARS-CoV-2 started from the PDB structure 6WX4 with the covalent inhibitor removed to generate an apo structure.
   

DESRES-ANTON-10906555

Release date: May 6th, 2020

  • A selection of 50 2 µs simulations of FDA approved or investigational drug molecules binding to a construct of the SARS-CoV-2 trimeric spike protein.
   

DESRES-ANTON-10918441

Release date: May 6th, 2020

  • A selection of 78 2 µs simulations of FDA approved or investigational drug molecules binding to the ectodomain of human ACE2.
   

DESRES-ANTON-11021566

Release date: May 1st, 2020

  • A 10 µs simulation of trimeric SARS-CoV-2 spike glycoprotein, initiated in the closed state (PDB 6VXX) with additional loop structures and glycan chains.
   

DESRES-ANTON-11021571

Release date: May 1st, 2020

  • A 10 µs simulation of trimeric SARS-CoV-2 spike glycoprotein, initiated in a partially opened state (PDB 6VYB) with additional loop structures and glycan chains.
   

DESRES-ANTON-10917618

Release date: April 15th, 2020

  • A 10 µs simulation of the SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex (PDB 6M71) starting with zoomed-in view of partially disordered N-terminal region of NiRAN domain folding into stable ordered structure that resembles N-lobe fold of protein kinases.
   

DESRES-ANTON-10875753

Release date: April 6th, 2020

  • A 10 µs simulation of human ACE2 ectodomain, initiated in an apo open state (PDB 1R42).
   

DESRES-ANTON-10875754

Release date: April 6th, 2020

  • A 10 µs simulation of human ACE2 ectodomain, initiated in an inhibitor-bound closed state (PDB 1R4L).
   

DESRES-ANTON-10875775

Release date: April 6th, 2020

  • A 10 µs simulation of human ACE2 in complex with the Receptor Binding Domain of spike protein from SARS-CoV-1 (PDB 2AJF).
   

DESRES-ANTON-10905033

Release date: April 6th, 2020

  • A 10 µs simulation of human ACE2 in complex with the Receptor Binding Domain of spike protein from SARS-CoV-2 (PDB 6M17).
   

DESRES-ANTON-10875755

Release date: April 6th, 2020

  • A 10 µs simulation of human ACE2 in complex with a chimera construct of the two coronaviruses SARS-CoV-1 and SARS-CoV-2 (PDB 6VW1).
   

DESRES-ANTON-10895671

Release date: April 3rd, 2020

  • Four representative trajectories containing binding events from an aggregate of 30 µs of Accelerated Weighted Ensemble sampling simulation with hundreds of binding and thousands of unbinding events.
   

DESRES-ANTON-10897136

Release date: March 27th, 2020

  • A 10 µs simulation of trimeric SARS-CoV-2 spike glycoprotein, initiated in the closed state (PDB 6VXX) (Note: superseded by DESRES-ANTON-11021566).
   

DESRES-ANTON-10897850

Release date: March 27th, 2020

  • A 10 µs simulation of trimeric SARS-CoV-2 spike glycoprotein, initiated in a partially opened state (PDB 6VYB) (Note: superseded by DESRES-ANTON-11021571).
   

DESRES-ANTON-10880334

Release date: March 27th, 2020

  • A 100 µs simulation of the main protease of SARS-CoV-2, a critical enzyme for the maturation of viral particles and a potential target for antiviral drugs, started from the apo enzyme structure determined by X-ray crystallography (PDB 6Y84).