SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)

Smith, Micholas Dean; Rogers, David; Vermaas, Josh; Smith, Jeremy C

doi:10.13139/olcf/1657844

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DOE OSTI · 1657844

SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)

Smith, Micholas Dean·Rogers, David·Vermaas, Josh·Smith, Jeremy C

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Abstract

Protein-only trajectories of the lowest-temperature window (310K) extracted from temperature replica-exchange molecular dynamics simulations of 23 different SARS CoV-2 systems, including S Protein ACE2-receptor binding-domain, MPro, PLPro, NSP3 ADRP (X-domain/macrodomain/phosphatase), NSP15 (endoribonuclease), NSP9, NSP10, NSP16, and N-protein N-terminus. Systems were prepared with charmm-gui and simulated using the GROMACS simulation software suite. Trajectories are provided in compressed dcd format with accompanying coordinate/topology files in pdb and psf formats. This data supplements the data release, DOI: 10.13139/OLCF/1650650 ('SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)')

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59 BASIC BIOLOGICAL SCIENCES 60 APPLIED LIFE SCIENCES 99 GENERAL AND MISCELLANEOUS COVID-19 gromacs molecular dynamics protein SARS CoV-2 coronavirus simulation T-REMD

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Smith, Micholas Dean, Rogers, David, Vermaas, Josh, Smith, Jeremy C. 2021-01-20. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories). https://doi.org/10.13139/olcf%2F1657844

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