September 25, 2020 Dataset Open Access

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

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{
  "description": "<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a&nbsp;dimeric transmembrane protein&nbsp;(PDB id: 6XDC, Bioassembly 1) embedded in a membrane&nbsp;patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion.&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.9b00435\">Barrera 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;</p>\n\n<p>The files contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing 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. Additionally, &nbsp;</p>\n\n<p>The files 6xdc_SIRAHcg_rawdata_0-2us.tar, 6xdc_SIRAHcg_rawdata_2-4us.tar, 6xdc_SIRAHcg_rawdata_4-6us.tar, 6xdc_SIRAHcg_rawdata_6-8us.tar, and 6xdc_SIRAHcg_rawdata_8-10us.tar 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;6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar&nbsp;contains only the protein and phospholipids&acute;&nbsp;coordinates, with&nbsp;one frame every 10ns.</p>\n\n<p>To take a quick look at the trajectory:</p>\n\n<p>1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar</p>\n\n<p>2- Open the trajectory on VMD using the command line:</p>\n\n<p>vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_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 Exequiel Barrera&nbsp;(ebarrera@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/0000-0002-0388-3078", 
      "@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/0000-0003-4099-9907", 
      "@type": "Person", 
      "name": "Florencia Klein"
    }, 
    {
      "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/4044378", 
  "datePublished": "2020-09-25", 
  "keywords": [
    "Coronavirus", 
    "drug design", 
    "simulation", 
    "SIRAH", 
    "coarse-grain", 
    "COVID-19", 
    "SARS"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
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  "identifier": "https://doi.org/10.5281/zenodo.4044378", 
  "@id": "https://doi.org/10.5281/zenodo.4044378", 
  "@type": "Dataset", 
  "name": "SIRAH-CoV2  initiative: Membrane embedded SARS-CoV-2 ORF3a  (PDB id:6XDC)"
}