Dataset Open Access

SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)

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": {
      "id": "CC-BY-4.0"
    }, 
    "title": "SIRAH-CoV2  initiative: Membrane embedded SARS-CoV-2 ORF3a  (PDB id:6XDC)", 
    "relations": {
      "version": [
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    "communities": [
      {
        "id": "covid-19"
      }, 
      {
        "id": "covid19-structure-hub"
      }, 
      {
        "id": "eradicatecovid19"
      }
    ], 
    "references": [
      "Barrera et al. JCTC 2019 (DOI:10.1021/acs.jctc.9b00435)", 
      "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", 
      "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"
    ], 
    "keywords": [
      "Coronavirus", 
      "drug design", 
      "simulation", 
      "SIRAH", 
      "coarse-grain", 
      "COVID-19", 
      "SARS"
    ], 
    "publication_date": "2020-09-25", 
    "creators": [
      {
        "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": "0000-0003-4099-9907", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Florencia Klein"
      }, 
      {
        "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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