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

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    <subfield code="a">Exequiel Barrera</subfield>
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    <subfield code="a">Matías Machado</subfield>
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    <subfield code="u">Institut Pasteur de Montevideo</subfield>
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    <subfield code="a">Florencia Klein</subfield>
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    <subfield code="a">SIRAH-CoV2  initiative:  RNA binding domain of nucleocapsid phosphoprotein  (PDB id:6VYO)</subfield>
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    <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>
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Publication date:
April 10, 2020
DOI:
10.5281/zenodo.3747621

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Keyword(s):
Coronavirus drug design simulation SIRAH coarse-grain Nucleocapsid COVID-19
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