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

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

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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)")

Authors:: Smith, Micholas Dean; Rogers, David; Vermaas, Josh; Smith, Jeremy C.

Publication Date:: Wed Jan 20 00:00:00 EST 2021

DOE Contract Number:: DE-AC05-00OR22725

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.

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                    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

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                    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

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@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         = {Wed Jan 20 00:00:00 EST 2021},

  month        = {Wed Jan 20 00:00:00 EST 2021}

}

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

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