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

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)")

Authors:
; ; ;
Publication Date:
DOE Contract Number:  
DE-AC05-00OR22725
Product Type:
Dataset
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); University of Tennessee, Knoxville, Knoxville, TN (United States)
Sponsoring Org.:
Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
Subject:
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
OSTI Identifier:
1657844
DOI:
https://doi.org/10.13139/OLCF/1657844

Citation Formats

Smith, Micholas Dean, Rogers, David, Vermaas, Josh, and Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories). United States: N. p., 2021. Web. doi:10.13139/OLCF/1657844.
Smith, Micholas Dean, Rogers, David, Vermaas, Josh, & Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories). United States. doi:https://doi.org/10.13139/OLCF/1657844
Smith, Micholas Dean, Rogers, David, Vermaas, Josh, and Smith, Jeremy C. 2021. "SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)". United States. doi:https://doi.org/10.13139/OLCF/1657844. https://www.osti.gov/servlets/purl/1657844. Pub date:Wed Jan 20 00:00:00 EST 2021
@article{osti_1657844,
title = {SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)},
author = {Smith, Micholas Dean and Rogers, David and Vermaas, Josh and Smith, Jeremy C.},
abstractNote = {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)")},
doi = {10.13139/OLCF/1657844},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2021},
month = {1}
}