SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)

Smith, Micholas Dean; Rogers, David; Vermaas, Josh; Smith, Jeremy C

doi:10.13139/OLCF/1657847

Title: SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)

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Abstract

Raw temperature replica-exchange molecular dyanmics trajectories 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. Non-demuxed, i.e. discontinuous/constant temperature window, trajectories are provided in compressed GROMACS xtc and full trr formats. This data supplements the data releases DOI: 10.13139/OLCF/160650 "SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)" & DOI: 10.13139/OLCF/1657844 "SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Extracted Protein Coordinate Trajectories)"

Authors:

Smith, Micholas Dean; Rogers, David; Vermaas, Josh; Smith, Jeremy C

ORNL-OLCF

Publication Date:: Tue Jan 19 23:00:00 EST 2021

DOE Contract Number:: AC05-00OR22725

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The 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; GROMACS, SARS-CoV2, Molecular Dynamics, T-REMD, Temperature Replica Exchange, COVID-19

OSTI Identifier:: 1657847

DOI:: https://doi.org/10.13139/OLCF/1657847

Citation Formats


                    Smith, Micholas Dean, Rogers, David, Vermaas, Josh, and Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories).  United States: N. p., 2021. 
        Web.  doi:10.13139/OLCF/1657847.

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                    Smith, Micholas Dean, Rogers, David, Vermaas, Josh, & Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories).  United States.  doi:https://doi.org/10.13139/OLCF/1657847

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                    Smith, Micholas Dean, Rogers, David, Vermaas, Josh, and Smith, Jeremy C. 2021.  
"SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)".  United States.  doi:https://doi.org/10.13139/OLCF/1657847.  https://www.osti.gov/servlets/purl/1657847. Pub date:Tue Jan 19 23:00:00 EST 2021

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@article{osti_1657847,

  title        = {SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)},

  author       = {Smith, Micholas Dean and Rogers, David and Vermaas, Josh and Smith, Jeremy C},

  abstractNote = {Raw temperature replica-exchange molecular dyanmics trajectories 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. Non-demuxed, i.e. discontinuous/constant temperature window, trajectories are provided in compressed GROMACS xtc and full trr formats. This data supplements the data releases DOI: 10.13139/OLCF/160650 "SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)" & DOI: 10.13139/OLCF/1657844 "SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Extracted Protein Coordinate Trajectories)"},

  doi          = {10.13139/OLCF/1657847},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Jan 19 23:00:00 EST 2021},

  month        = {Tue Jan 19 23:00:00 EST 2021}

}

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DOI: https://doi.org/10.13139/OLCF/1657847

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