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

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

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 resources

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)

Related resources

Details

DOI

10.13139/OLCF/1657844

Release date

January 20, 2021

Dataset

Dataset type

AS Animations/Simulations

Software

GROMACS (version 2020.1 or greater); VMD

Acknowledgements

Papers using this dataset are requested to include the following text in their acknowledgements:

*Support for 10.13139/OLCF/1657844 is provided by the U.S. Department of Energy, project BIF128 under Contract DE-AC05-00OR22725. This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility.

Category

  • 59 BASIC BIOLOGICAL SCIENCES,
  • 60 APPLIED LIFE SCIENCES,
  • 99 GENERAL AND MISCELLANEOUS

Keywords

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