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

    Micholas Dean Smith | Oak Ridge National Laboratory
    David Rogers | Oak Ridge National Laboratory
    Josh Vermaas | Oak Ridge National Laboratory
    Jeremy C Smith | Oak Ridge National Laboratory/UTK

Description

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)')

Funding Information

DOE Contract Number

DE-AC05-00OR22725

Originating Research Organization

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);University of Tennessee, Knoxville, Knoxville, TN (United States)

Sponsoring Organization

Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)

Project Identifier

BIF128

Related Works

Details

DOI

https://doi.org/10.13139/OLCF/1657844

Release Date

January 20, 2021

Subject

BASIC BIOLOGICAL SCIENCES, APPLIED LIFE SCIENCES, GENERAL AND MISCELLANEOUS

Keywords

SARS CoV-2 coronavirus, protein, simulation, gromacs, molecular dynamics, T-REMD, COVID-19

Dataset

Dataset Type

AS Animations/Simulations

Software

GROMACS (version 2020.1 or greater); VMD

Cite This Dataset:

Smith, M., Rogers, D., Vermaas, J., Smith, J. (2021). SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories). Oak Ridge National Laboratory. https://doi.org/10.13139/OLCF/1657844.

Acknowledgements

This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Advanced Scientific Computing Research programs in the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.