Dataset Open Access

SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)

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


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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
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  "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>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0003-4099-9907", 
      "@type": "Person", 
      "name": "Florencia Klein"
    }, 
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0002-0388-3078", 
      "@type": "Person", 
      "name": "Exequiel Barrera"
    }, 
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0001-6604-0329", 
      "@type": "Person", 
      "name": "Pablo Garay"
    }, 
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0002-9971-4710", 
      "@type": "Person", 
      "name": "Mat\u00edas Machado"
    }, 
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0003-3872-6117", 
      "@type": "Person", 
      "name": "Mart\u00edn So\u00f1ora"
    }, 
    {
      "affiliation": "Institut Pasteur de Montevideo", 
      "@id": "https://orcid.org/0000-0001-6435-4543", 
      "@type": "Person", 
      "name": "Sergio Pantano"
    }
  ], 
  "url": "https://zenodo.org/record/3766270", 
  "datePublished": "2020-04-25", 
  "version": "SIRAH version 2.2, Amber18", 
  "keywords": [
    "Coronavirus", 
    "drug design", 
    "simulation", 
    "SIRAH", 
    "coarse-grain", 
    "CoV2 Papain-like Protease", 
    "COVID-19", 
    "SARS", 
    "Molecular Dynamics"
  ], 
  "@context": "https://schema.org/", 
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      "contentUrl": "https://zenodo.org/api/files/9fc87fe3-0e5a-413d-a016-46d25e0eef03/6W9C_SIRAHcg_10us_prot_skip10ns.tar", 
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  "identifier": "https://doi.org/10.5281/zenodo.3766270", 
  "@id": "https://doi.org/10.5281/zenodo.3766270", 
  "@type": "Dataset", 
  "name": "SIRAH-CoV2  initiative:  Papain-like Protease   (PDB id:6W9C)"
}
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