June 22, 2020 Dataset Open Access

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

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  <identifier identifierType="DOI">10.5281/zenodo.3903522</identifier>
  <creators>
    <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>Exequiel Barrera</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0388-3078</nameIdentifier>
      <affiliation>Institut Pasteur de Montevideo</affiliation>
    </creator>
    <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>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: Glycosylated RBD</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Coronavirus</subject>
    <subject>simulation</subject>
    <subject>glycosylation</subject>
    <subject>SIRAH</subject>
    <subject>coarse-grain</subject>
    <subject>COVID-19</subject>
    <subject>SARS</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-06-22</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3903522</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3903521</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 2.3, 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 trajectories of&amp;nbsp;10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike&amp;acute;s RBD glycosylated at Asn331&amp;nbsp;and Asn343. The initial coordinates correspond to amino acids 327 to 532&amp;nbsp;taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI (http://www.charmm-gui.org).&lt;/p&gt;

&lt;p&gt;There are two different sets of simulations corresponding to Core Complex and High Mannose. 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&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;. Glycan parameters&amp;nbsp;are available upon request.&lt;/p&gt;

&lt;p&gt;The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and&amp;nbsp;RBD-Man9_SIRAHcg_rawdata_6-10us.tar,&amp;nbsp;contain&amp;nbsp;all the raw information required to visualize (on VMD), analyze, and backmap the simulations of High Mannose glycosylated RBD. Analogous information for Core-complex glycosylations is contained in files&amp;nbsp;RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and&amp;nbsp;RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar&lt;/p&gt;

&lt;p&gt;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, files with names ending in SIRAHcg_10us_glycoprot.tar contain only the protein coordinates, while file names ending with&amp;nbsp; SIRAHcg_10us_glycoprot_skip10ns.tar contains one frame every 10ns.&lt;/p&gt;

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

&lt;p&gt;1- Untar&amp;nbsp;the file&amp;nbsp;RBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar&lt;/p&gt;

&lt;p&gt;2- Open the trajectory on VMD 1.9.3 using the command line:&lt;/p&gt;

&lt;p&gt;vmd glyco-RBD_SIRAHcg_glycoprot.prmtop glyco-RBD_SIRAHcg_glycoprot.ncrst glyco-RBD_SIRAHcg_glycoprot_10us_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 Pablo Garay (pgaray@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 JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado &amp; Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"]}</description>
  </descriptions>
</resource>