There is a newer version of this record available.

Dataset Open Access

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.


JSON-LD (schema.org) Export

{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>This dataset contains the trajectories&nbsp;of&nbsp;10&nbsp;microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the&nbsp;single mutant D614G, and the double mutant T307I/D614G. Simulations are based&nbsp;on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were&nbsp;performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo&nbsp;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 following files in gromacs format are provided for each simulation:</p>\n\n<p>i) a .psf containing the topological information (connectivity, etc),&nbsp;</p>\n\n<p>ii) a topology (.top)</p>\n\n<p>ii) a big&nbsp;.xtc file containing&nbsp;10 microseconds of the CG protein&nbsp;recorded every 200 picoseconds&nbsp;(50000 frames)</p>\n\n<p>iii) a smaller .xtc file containing&nbsp;the same trajectory but with only one frame per nanosecond&nbsp;(1000 frames)</p>\n\n<p>iv) a .gro file with the initial configuration</p>\n\n<p>Finally, the file&nbsp;sirah_vmdtk.tcl contains a series of macros and scripts that facilitate&nbsp;the visualization and&nbsp;analysis of the CG trajaectories.&nbsp;Step-By-Step tutorials for&nbsp;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>To take a quick look at a trajectory using VMD 1.9.3, run the command:</p>\n\n<p>&gt; vmd SpikeWT-SIRAH.psf SpikeWT-SIRAH.gro&nbsp;SpikeWT-SIRAH-1kfrm.xtc -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 for data sharing.</p>\n\n<p>For further details, please contact&nbsp;Sergio Pantano (spantano@pasteur.edu.uy).</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Escuela de Medicina, and Centro Asistencial Docente y de Investigaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Gonz\u00e1lez-Puelma, Jorge"
    }, 
    {
      "affiliation": "Departamento de Ingenier\u00eda en Computaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Aldridge, Jacqueline"
    }, 
    {
      "affiliation": "Departamento de Ingenier\u00eda en Computaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Montes de Oca, Marco"
    }, 
    {
      "affiliation": "Escuela de Medicina, Centro Asistencial Docente y de Investigaci\u00f3n, Universidad de Magallanes, Enfermedades Infecciosas, Hospital Cl\u00ednico de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Pinto , M\u00f3nica"
    }, 
    {
      "affiliation": "Departamento de Ingenier\u00eda en Computaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Uribe-Paredes, Roberto"
    }, 
    {
      "affiliation": "Departamento de Matem\u00e1tica y F\u00edsica, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Fern\u00e1ndez-Goycoolea, Jos\u00e9"
    }, 
    {
      "affiliation": "Escuela de Medicina, Centro Asistencial Docente y de Investigaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Alvarez Saravia, Diego"
    }, 
    {
      "affiliation": "Escuela de Medicina, Centro Asistencial Docente y de Investigaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "\u00c1lvarez, Hermy"
    }, 
    {
      "affiliation": "Centro de Gen\u00e9tica y Gen\u00f3mica, Instituto de Ciencias e Innovaci\u00f3n en Medicina, Facultad de Medicina Cl\u00ednica Alemana, Universidad del Desarrollo, Chile", 
      "@type": "Person", 
      "name": "Encina, Gonzalo"
    }, 
    {
      "affiliation": "Laboratorio Cl\u00ednico, Cl\u00ednica Alemana de Santiago, Facultad de Medicina Cl\u00ednica Alemana, Universidad del Desarrollo, Santiago, and Instituto de Ciencias e Innovaci\u00f3n en Medicina (ICIM), Universidad del Desarrollo, Santiago, Chile", 
      "@type": "Person", 
      "name": "Weitzel, Thomas"
    }, 
    {
      "affiliation": "Escuela de Medicina, Universidad de Magallanes, and Enfermedades Infecciosas, Hospital Cl\u00ednico de Magallanes, Chile.", 
      "@type": "Person", 
      "name": "Mu\u00f1oz, Rodrigo"
    }, 
    {
      "affiliation": "Centre for Biotechnology and Bioengineering, Universidad de Chile, and Facultad de Ciencias, F\u00edsicas y Matem\u00e1ticas, Universidad de Chile.", 
      "@type": "Person", 
      "name": "Olivera-Nappa, \u00c1lvaro"
    }, 
    {
      "affiliation": "Biomolecular Simulations Group, Institut Pasteur de Montevideo, Uruguay.", 
      "@id": "https://orcid.org/0000-0001-6435-4543", 
      "@type": "Person", 
      "name": "Pantano, Sergio"
    }, 
    {
      "affiliation": "Escuela de Medicina, and Centro Asistencial Docente y de Investigaci\u00f3n, Universidad de Magallanes, Chile", 
      "@type": "Person", 
      "name": "Navarrete, Marcelo A."
    }
  ], 
  "url": "https://zenodo.org/record/4725931", 
  "datePublished": "2021-04-28", 
  "keywords": [
    "SARS-CoV2", 
    "Variants", 
    "Covid-19", 
    "Coarse-Grained Simulation", 
    "Chile", 
    "sub-Antarctic"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/8da096ca-8331-412d-9aeb-f445f5ccb871/SpikeD614G-SIRAH-1kfrm.xtc", 
      "encodingFormat": "xtc", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/8da096ca-8331-412d-9aeb-f445f5ccb871/SpikeD614G-SIRAH-50kfrm.xtc", 
      "encodingFormat": "xtc", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/8da096ca-8331-412d-9aeb-f445f5ccb871/SpikeD614G-SIRAH.psf", 
      "encodingFormat": "psf", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.4725931", 
  "@id": "https://doi.org/10.5281/zenodo.4725931", 
  "@type": "Dataset", 
  "name": "SIRAH-CoV2  initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile"
}
139
60
views
downloads
All versions This version
Views 13913
Downloads 604
Data volume 47.5 GB3.4 GB
Unique views 11511
Unique downloads 211

Share

Cite as