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SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile

González-Puelma, Jorge; Aldridge, Jacqueline; Montes de Oca, Marco; Pinto , Mónica; Uribe-Paredes, Roberto; Fernández-Goycoolea, José; Alvarez Saravia, Diego; Álvarez, Hermy; Encina, Gonzalo; Weitzel, Thomas; Muñoz, Rodrigo; Olivera-Nappa, Álvaro; Pantano, Sergio; Navarrete, Marcelo A.


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  <identifier identifierType="DOI">10.5281/zenodo.4725931</identifier>
  <creators>
    <creator>
      <creatorName>González-Puelma, Jorge</creatorName>
      <givenName>Jorge</givenName>
      <familyName>González-Puelma</familyName>
      <affiliation>Escuela de Medicina, and Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Aldridge, Jacqueline</creatorName>
      <givenName>Jacqueline</givenName>
      <familyName>Aldridge</familyName>
      <affiliation>Departamento de Ingeniería en Computación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Montes de Oca, Marco</creatorName>
      <givenName>Marco</givenName>
      <familyName>Montes de Oca</familyName>
      <affiliation>Departamento de Ingeniería en Computación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Pinto , Mónica</creatorName>
      <givenName>Mónica</givenName>
      <familyName>Pinto</familyName>
      <affiliation>Escuela de Medicina, Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Enfermedades Infecciosas, Hospital Clínico de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Uribe-Paredes, Roberto</creatorName>
      <givenName>Roberto</givenName>
      <familyName>Uribe-Paredes</familyName>
      <affiliation>Departamento de Ingeniería en Computación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Fernández-Goycoolea, José</creatorName>
      <givenName>José</givenName>
      <familyName>Fernández-Goycoolea</familyName>
      <affiliation>Departamento de Matemática y Física, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Alvarez Saravia, Diego</creatorName>
      <givenName>Diego</givenName>
      <familyName>Alvarez Saravia</familyName>
      <affiliation>Escuela de Medicina, Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Álvarez, Hermy</creatorName>
      <givenName>Hermy</givenName>
      <familyName>Álvarez</familyName>
      <affiliation>Escuela de Medicina, Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Encina, Gonzalo</creatorName>
      <givenName>Gonzalo</givenName>
      <familyName>Encina</familyName>
      <affiliation>Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Weitzel, Thomas</creatorName>
      <givenName>Thomas</givenName>
      <familyName>Weitzel</familyName>
      <affiliation>Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, and Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago, Chile</affiliation>
    </creator>
    <creator>
      <creatorName>Muñoz, Rodrigo</creatorName>
      <givenName>Rodrigo</givenName>
      <familyName>Muñoz</familyName>
      <affiliation>Escuela de Medicina, Universidad de Magallanes, and Enfermedades Infecciosas, Hospital Clínico de Magallanes, Chile.</affiliation>
    </creator>
    <creator>
      <creatorName>Olivera-Nappa, Álvaro</creatorName>
      <givenName>Álvaro</givenName>
      <familyName>Olivera-Nappa</familyName>
      <affiliation>Centre for Biotechnology and Bioengineering, Universidad de Chile, and Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile.</affiliation>
    </creator>
    <creator>
      <creatorName>Pantano, Sergio</creatorName>
      <givenName>Sergio</givenName>
      <familyName>Pantano</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6435-4543</nameIdentifier>
      <affiliation>Biomolecular Simulations Group, Institut Pasteur de Montevideo, Uruguay.</affiliation>
    </creator>
    <creator>
      <creatorName>Navarrete, Marcelo A.</creatorName>
      <givenName>Marcelo A.</givenName>
      <familyName>Navarrete</familyName>
      <affiliation>Escuela de Medicina, and Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Chile</affiliation>
    </creator>
  </creators>
  <titles>
    <title>SIRAH-CoV2  initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>SARS-CoV2</subject>
    <subject>Variants</subject>
    <subject>Covid-19</subject>
    <subject>Coarse-Grained Simulation</subject>
    <subject>Chile</subject>
    <subject>sub-Antarctic</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-04-28</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4725931</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4725930</relatedIdentifier>
  </relatedIdentifiers>
  <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&amp;nbsp;of&amp;nbsp;10&amp;nbsp;microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the&amp;nbsp;single mutant D614G, and the double mutant T307I/D614G. Simulations are based&amp;nbsp;on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were&amp;nbsp;performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo&amp;nbsp;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;&lt;/p&gt;

&lt;p&gt;The following files in gromacs format are provided for each simulation:&lt;/p&gt;

&lt;p&gt;i) a .psf containing the topological information (connectivity, etc),&amp;nbsp;&lt;/p&gt;

&lt;p&gt;ii) a topology (.top)&lt;/p&gt;

&lt;p&gt;ii) a big&amp;nbsp;.xtc file containing&amp;nbsp;10 microseconds of the CG protein&amp;nbsp;recorded every 200 picoseconds&amp;nbsp;(50000 frames)&lt;/p&gt;

&lt;p&gt;iii) a smaller .xtc file containing&amp;nbsp;the same trajectory but with only one frame per nanosecond&amp;nbsp;(1000 frames)&lt;/p&gt;

&lt;p&gt;iv) a .gro file with the initial configuration&lt;/p&gt;

&lt;p&gt;Finally, the file&amp;nbsp;sirah_vmdtk.tcl contains a series of macros and scripts that facilitate&amp;nbsp;the visualization and&amp;nbsp;analysis of the CG trajaectories.&amp;nbsp;Step-By-Step tutorials for&amp;nbsp;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;To take a quick look at a trajectory using VMD 1.9.3, run the command:&lt;/p&gt;

&lt;p&gt;&amp;gt; vmd SpikeWT-SIRAH.psf SpikeWT-SIRAH.gro&amp;nbsp;SpikeWT-SIRAH-1kfrm.xtc -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 for data sharing.&lt;/p&gt;

&lt;p&gt;For further details, please contact&amp;nbsp;Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</description>
  </descriptions>
</resource>
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