Dataset Open Access

SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)

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


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/759f2c4a-9177-4ef5-8807-f435765854a5/6WIQ_SIRAHcg_10us_prot_skip10ns.tar"
      }, 
      "checksum": "md5:321dd648caeccaed542e583169be8a40", 
      "bucket": "759f2c4a-9177-4ef5-8807-f435765854a5", 
      "key": "6WIQ_SIRAHcg_10us_prot_skip10ns.tar", 
      "type": "tar", 
      "size": 23429120
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/759f2c4a-9177-4ef5-8807-f435765854a5/6WIQ_SIRAHcg_10us_prot.tar"
      }, 
      "checksum": "md5:74dc9e93df42b24270a8a901cbaca0ee", 
      "bucket": "759f2c4a-9177-4ef5-8807-f435765854a5", 
      "key": "6WIQ_SIRAHcg_10us_prot.tar", 
      "type": "tar", 
      "size": 1129072640
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/759f2c4a-9177-4ef5-8807-f435765854a5/6WIQ_SIRAHcg_rawdata_0-5us.tar"
      }, 
      "checksum": "md5:254c2fc9be75b8255faa56e46304b822", 
      "bucket": "759f2c4a-9177-4ef5-8807-f435765854a5", 
      "key": "6WIQ_SIRAHcg_rawdata_0-5us.tar", 
      "type": "tar", 
      "size": 5736714240
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/759f2c4a-9177-4ef5-8807-f435765854a5/6WIQ_SIRAHcg_rawdata_5-10us.tar"
      }, 
      "checksum": "md5:3c1363561cfaa2af654f45ba3b81bfbb", 
      "bucket": "759f2c4a-9177-4ef5-8807-f435765854a5", 
      "key": "6WIQ_SIRAHcg_rawdata_5-10us.tar", 
      "type": "tar", 
      "size": 5736714240
    }
  ], 
  "owners": [
    96953
  ], 
  "doi": "10.5281/zenodo.3820673", 
  "stats": {
    "version_unique_downloads": 17.0, 
    "unique_views": 723.0, 
    "views": 771.0, 
    "version_views": 771.0, 
    "unique_downloads": 17.0, 
    "version_unique_views": 723.0, 
    "volume": 58568867840.0, 
    "version_downloads": 22.0, 
    "downloads": 22.0, 
    "version_volume": 58568867840.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3820673", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.3820672", 
    "bucket": "https://zenodo.org/api/files/759f2c4a-9177-4ef5-8807-f435765854a5", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.3820672.svg", 
    "html": "https://zenodo.org/record/3820673", 
    "latest_html": "https://zenodo.org/record/3820673", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3820673.svg", 
    "latest": "https://zenodo.org/api/records/3820673"
  }, 
  "conceptdoi": "10.5281/zenodo.3820672", 
  "created": "2020-05-12T21:24:34.605769+00:00", 
  "updated": "2021-01-13T17:15:57.104786+00:00", 
  "conceptrecid": "3820672", 
  "revision": 6, 
  "id": 3820673, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3820673", 
    "description": "<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ).&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;</p>\n\n<p>The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar, contain&nbsp;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&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;6WIQ_SIRAHcg_10us_prot.tar&nbsp;contains only the protein coordinates, while&nbsp;6WIQ_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;6WIQ_SIRAHcg_10us_prot_skip10ns.tar</p>\n\n<p>2- Open the trajectory on VMD using the command line:</p>\n\n<p>vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_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 Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>", 
    "language": "eng", 
    "title": "SIRAH-CoV2  initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "3820672"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "3820673"
          }
        }
      ]
    }, 
    "communities": [
      {
        "id": "covid-19"
      }, 
      {
        "id": "zenodo"
      }
    ], 
    "version": "SIRAH version 2.2, Amber18", 
    "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)"
    ], 
    "keywords": [
      "Coronavirus", 
      "drug design", 
      "simulation", 
      "SIRAH", 
      "coarse-grain", 
      "CoV2 NSP7-NSP8", 
      "SARS"
    ], 
    "publication_date": "2020-05-11", 
    "creators": [
      {
        "orcid": "0000-0003-4099-9907", 
        "affiliation": "Institut Pasteur de Montevideo", 
        "name": "Florencia Klein"
      }, 
      {
        "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": "0000-0002-9971-4710", 
        "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"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.1021/acs.jctc.9b00006", 
        "relation": "cites", 
        "resource_type": "publication-article"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.1021/acs.jctc.9b00953", 
        "relation": "cites", 
        "resource_type": "publication-article"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3820672", 
        "relation": "isVersionOf"
      }
    ]
  }
}
771
22
views
downloads
All versions This version
Views 771771
Downloads 2222
Data volume 58.6 GB58.6 GB
Unique views 723723
Unique downloads 1717

Share

Cite as