Dataset Open Access

SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)

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


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  <identifier identifierType="DOI">10.5281/zenodo.3766270</identifier>
  <creators>
    <creator>
      <creatorName>Florencia Klein</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-4099-9907</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <creator>
      <creatorName>Exequiel Barrera</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0388-3078</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <creator>
      <creatorName>Pablo Garay</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6604-0329</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <creator>
      <creatorName>Matías Machado</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9971-4710</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <creator>
      <creatorName>Martín Soñora</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3872-6117</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <creator>
      <creatorName>Sergio Pantano</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6435-4543</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
  </creators>
  <titles>
    <title>SIRAH-CoV2  initiative:  Papain-like Protease   (PDB id:6W9C)</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Coronavirus</subject>
    <subject>drug design</subject>
    <subject>simulation</subject>
    <subject>SIRAH</subject>
    <subject>coarse-grain</subject>
    <subject>CoV2 Papain-like Protease</subject>
    <subject>COVID-19</subject>
    <subject>SARS</subject>
    <subject>Molecular Dynamics</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-04-25</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3766270</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3766269</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>SIRAH version 2.2, Amber18</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C).&amp;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&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006"&gt;Machado et al. JCTC 2019&lt;/a&gt;, adding 150 mM NaCl according to&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953"&gt;Machado &amp;amp; Pantano JCTC 2020&lt;/a&gt;.&amp;nbsp;Zinc ions were parameterized as reported in&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160"&gt;Klein et al. 2020&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;The files 6W9C_SIRAHcg_rawdata_0-5us.tar, &amp;nbsp;6W9C_SIRAHcg_rawdata_5-10us.tar,&amp;nbsp;contain&amp;nbsp;all the raw information required to visualize (on VMD), analyze,&amp;nbsp;backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing&amp;nbsp;CG trajectories using&amp;nbsp;&lt;a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152"&gt;SirahTools&lt;/a&gt;&amp;nbsp;can be found at www.sirahff.com.&lt;/p&gt;

&lt;p&gt;Additionally, the&amp;nbsp;file&amp;nbsp;6W9C_SIRAHcg_10us_prot.tar&amp;nbsp;contains only the protein coordinates, while&amp;nbsp;6W9C_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.&lt;/p&gt;

&lt;p&gt;To take a quick look at the trajectory:&lt;/p&gt;

&lt;p&gt;1- Untar&amp;nbsp;the file&amp;nbsp;6W9C_SIRAHcg_10us_prot_skip10ns.tar&lt;/p&gt;

&lt;p&gt;2- Open the trajectory on VMD using the command line:&lt;/p&gt;

&lt;p&gt;vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst 6W9C_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl&lt;/p&gt;

&lt;p&gt;Note that you can use normal VMD drawing methods as vdw, licorice, etc.,&amp;nbsp;and coloring by&amp;nbsp;restype, element, name, etc.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;This dataset is part of the SIRAH-CoV2&amp;nbsp;initiative.&lt;/p&gt;

&lt;p&gt;For further details, please contact Florencia&amp;nbsp;Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado &amp; Pantano. Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", "Machado &amp; Pantano. JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Klein et al. JCIM, 2020 (DOI:10.1021/acs.jcim.0c00160)"]}</description>
  </descriptions>
</resource>
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