Dataset Open Access

SIRAH-CoV2 initiative: RNA binding domain of nucleocapsid phosphoprotein (PDB id:6VYO)

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


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="x">Machado &amp; Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="x">Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="x">Machado &amp; Pantano,  Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="x">Klein et al. 2020, JCIM (DOI:10.1021/acs.jcim.0c00160)</subfield>
  </datafield>
  <datafield tag="041" ind1=" " ind2=" ">
    <subfield code="a">eng</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Coronavirus</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">drug design</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">simulation</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">SIRAH</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">coarse-grain</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Nucleocapsid</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">COVID-19</subfield>
  </datafield>
  <controlfield tag="005">20210113163000.0</controlfield>
  <controlfield tag="001">3747621</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0002-0388-3078</subfield>
    <subfield code="a">Exequiel Barrera</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0001-6604-0329</subfield>
    <subfield code="a">Pablo Garay</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0002-9971-4710</subfield>
    <subfield code="a">Matías Machado</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0003-3872-6117</subfield>
    <subfield code="a">Martín Soñora</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0001-6435-4543</subfield>
    <subfield code="a">Sergio Pantano</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">1447997440</subfield>
    <subfield code="z">md5:5f1193df2c44b1280859269896b46d8c</subfield>
    <subfield code="u">https://zenodo.org/record/3747621/files/6VYO_SIRAHcg_10us_prot.tar</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">30054400</subfield>
    <subfield code="z">md5:f384d0e452240734b73267f7314582c8</subfield>
    <subfield code="u">https://zenodo.org/record/3747621/files/6VYO_SIRAHcg_prot_10us_skip10ns.tar</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">7708005435</subfield>
    <subfield code="z">md5:3706c2ad21232fb4f1fe9cc4fa3645d3</subfield>
    <subfield code="u">https://zenodo.org/record/3747621/files/6VYO_SIRAHcg_rawdata.tar</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2020-04-10</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire_data</subfield>
    <subfield code="p">user-covid-19</subfield>
    <subfield code="p">user-zenodo</subfield>
    <subfield code="o">oai:zenodo.org:3747621</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur de Montevideo</subfield>
    <subfield code="0">(orcid)0000-0003-4099-9907</subfield>
    <subfield code="a">Florencia Klein</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">SIRAH-CoV2  initiative:  RNA binding domain of nucleocapsid phosphoprotein  (PDB id:6VYO)</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-covid-19</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-zenodo</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA binding domain of the nucleocapsid phosphoprotein in its APO form with Zn ions bound (PDB id:6VYO, Bioassembly 1). 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;. 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 file&amp;nbsp;6VYO_SIRAHcg_rawdata.tar&amp;nbsp;contains 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 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.&amp;nbsp;Additionally, the&amp;nbsp;file&amp;nbsp;6VYO_SIRAHcg_10us_prot.tar&amp;nbsp;contains only the protein coordinates, while&amp;nbsp;6VYO_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;6VYO_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&amp;nbsp;6VYO_SIRAHcg_prot_10us_skip10ns.prmtop 6VYO_SIRAHcg_prot_10us_skip10ns.ncrst 6VYO_SIRAHcg_prot_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., 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 Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.3747620</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.3747621</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">dataset</subfield>
  </datafield>
</record>
790
90
views
downloads
All versions This version
Views 790790
Downloads 9090
Data volume 257.6 GB257.6 GB
Unique views 754754
Unique downloads 5858

Share

Cite as