April 25, 2020 Dataset Open Access

Florencia Klein; Exequiel Barrera; Pablo Garay; Matías Machado; Martín Soñora; Sergio Pantano

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    "doi": "10.5281/zenodo.3766270", 
    "description": "<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C).&nbsp;Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in&nbsp;<a href=\"https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006\">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to&nbsp;<a href=\"https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953\">Machado &amp; Pantano JCTC 2020</a>.&nbsp;Zinc ions were parameterized as reported in&nbsp;<a href=\"https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160\">Klein et al. 2020</a>.</p>\n\n<p>The files 6W9C_SIRAHcg_rawdata_0-5us.tar, &nbsp;6W9C_SIRAHcg_rawdata_5-10us.tar,&nbsp;contain&nbsp;all the raw information required to visualize (on VMD), analyze,&nbsp;backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing&nbsp;CG trajectories using&nbsp;<a href=\"https://academic.oup.com/bioinformatics/article/32/10/1568/1743152\">SirahTools</a>&nbsp;can be found at www.sirahff.com.</p>\n\n<p>Additionally, the&nbsp;file&nbsp;6W9C_SIRAHcg_10us_prot.tar&nbsp;contains only the protein coordinates, while&nbsp;6W9C_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p>\n\n<p>To take a quick look at the trajectory:</p>\n\n<p>1- Untar&nbsp;the file&nbsp;6W9C_SIRAHcg_10us_prot_skip10ns.tar</p>\n\n<p>2- Open the trajectory on VMD using the command line:</p>\n\n<p>vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst 6W9C_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p>\n\n<p>Note that you can use normal VMD drawing methods as vdw, licorice, etc.,&nbsp;and coloring by&nbsp;restype, element, name, etc.&nbsp;</p>\n\n<p>This dataset is part of the SIRAH-CoV2&nbsp;initiative.</p>\n\n<p>For further details, please contact Florencia&nbsp;Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>", 
    "language": "eng", 
    "title": "SIRAH-CoV2  initiative:  Papain-like Protease   (PDB id:6W9C)", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
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    "version": "SIRAH version 2.2, Amber18", 
    "references": [
      "Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", 
      "Machado & Pantano. Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", 
      "Machado & Pantano. JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", 
      "Klein et al. JCIM, 2020 (DOI:10.1021/acs.jcim.0c00160)"
    ], 
    "keywords": [
      "Coronavirus", 
      "drug design", 
      "simulation", 
      "SIRAH", 
      "coarse-grain", 
      "CoV2 Papain-like Protease", 
      "COVID-19", 
      "SARS", 
      "Molecular Dynamics"
    ], 
    "publication_date": "2020-04-25", 
    "creators": [
      {
        "orcid": "0000-0003-4099-9907", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Florencia Klein"
      }, 
      {
        "orcid": "0000-0002-0388-3078", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Exequiel Barrera"
      }, 
      {
        "orcid": "0000-0001-6604-0329", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Pablo Garay"
      }, 
      {
        "orcid": "0000-0002-9971-4710", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mat\u00edas Machado"
      }, 
      {
        "orcid": "0000-0003-3872-6117", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mart\u00edn So\u00f1ora"
      }, 
      {
        "orcid": "0000-0001-6435-4543", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Sergio Pantano"
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