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
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-AC05-00OR22725Originating 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
- IsSupplementTo (DOI): https://doi.org/10.13139/OLCF/160650
Details
DOI
10.13139/OLCF/1657844Release date
January 20, 2021Dataset
Dataset type
AS Animations/SimulationsSoftware
GROMACS (version 2020.1 or greater); VMDAcknowledgements
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