Dataset Open Access

SIRAH-CoV2 initiative: RNA binding domain of nucleocapsid phosphoprotein (PDB id:6VYO)

Florencia Klein; Exequiel Barrera; Pablo Garay; 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 SARS-CoV2 RNA binding domain of the nucleocapsid phosphoprotein in its APO form with Zn ions bound (PDB id:6VYO, Bioassembly 1). Simulations were 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>. 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 file&nbsp;6VYO_SIRAHcg_rawdata.tar&nbsp;contains 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.&nbsp;Additionally, the&nbsp;file&nbsp;6VYO_SIRAHcg_10us_prot.tar&nbsp;contains only the protein coordinates, while&nbsp;6VYO_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;6VYO_SIRAHcg_10us_prot_skip10ns.tar</p>\n\n<p>2- Open the trajectory on VMD using the command line:</p>\n\n<p>vmd&nbsp;6VYO_SIRAHcg_prot_10us_skip10ns.prmtop 6VYO_SIRAHcg_prot_10us_skip10ns.ncrst 6VYO_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p>\n\n<p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., 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 Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>", 
    "language": "eng", 
    "title": "SIRAH-CoV2  initiative:  RNA binding domain of nucleocapsid phosphoprotein  (PDB id:6VYO)", 
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    "references": [
      "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", 
      "Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", 
      "Machado & Pantano,  Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", 
      "Klein et al. 2020, JCIM (DOI:10.1021/acs.jcim.0c00160)"
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    "keywords": [
      "Coronavirus", 
      "drug design", 
      "simulation", 
      "SIRAH", 
      "coarse-grain", 
      "Nucleocapsid", 
      "COVID-19"
    ], 
    "publication_date": "2020-04-10", 
    "creators": [
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        "orcid": "0000-0003-4099-9907", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Florencia Klein"
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        "orcid": "0000-0002-0388-3078", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Exequiel Barrera"
      }, 
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        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Pablo Garay"
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        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mat\u00edas Machado"
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        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mart\u00edn So\u00f1ora"
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        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Sergio Pantano"
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