Dataset Open Access

SIRAH-CoV2 initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41)

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


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    "description": "<p>This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41).&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>. Glycans have been removed from the structures.</p>\n\n<p>The file&nbsp;6W41_SIRAHcg_rawdata.tar contains 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;6W41_SIRAHcg_12us_prot.tar&nbsp;contains only the protein coordinates, while&nbsp;6W41_SIRAHcg_12us_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;6W41_SIRAHcg_12us_prot_skip10ns.tar</p>\n\n<p>2- Open the trajectory on VMD using the command line:</p>\n\n<p>vmd 6w41_SIRAHcg_prot.prmtop 6w41_SIRAHcg_prot.ncrst 6w41_SIRAHcg_prot_12us_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 Mart&iacute;n So&ntilde;ora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>", 
    "language": "eng", 
    "title": "SIRAH-CoV2  initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41)", 
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    "references": [
      "Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", 
      "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", 
      "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"
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    "keywords": [
      "Coronavirus", 
      "drug design", 
      "simulation", 
      "SIRAH", 
      "coarse-grain", 
      "CoV2 RBD", 
      "SARS", 
      "antibody"
    ], 
    "publication_date": "2020-04-30", 
    "creators": [
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        "orcid": "0000-0003-3872-6117", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mart\u00edn So\u00f1ora"
      }, 
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        "orcid": "0000-0002-0388-3078", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Exequiel Barrera"
      }, 
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        "orcid": "0000-0001-6604-0329", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Pablo Garay"
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        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Florencia Klein"
      }, 
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        "orcid": "0000-0002-9971-4710", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Mat\u00edas Machado"
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        "affiliation": "Institut Pasteur de Montevideo", 
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