Dataset Open Access

SIRAH-CoV2 initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41)

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

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        <foaf:name>Matías Machado</foaf:name>
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    <dct:title>SIRAH-CoV2 initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41)</dct:title>
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    <dcat:keyword>Coronavirus</dcat:keyword>
    <dcat:keyword>drug design</dcat:keyword>
    <dcat:keyword>simulation</dcat:keyword>
    <dcat:keyword>SIRAH</dcat:keyword>
    <dcat:keyword>coarse-grain</dcat:keyword>
    <dcat:keyword>CoV2 RBD</dcat:keyword>
    <dcat:keyword>SARS</dcat:keyword>
    <dcat:keyword>antibody</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-04-30</dct:issued>
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    <dct:description>&lt;p&gt;This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41).&amp;nbsp;Simulations have been 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;. Glycans have been removed from the structures.&lt;/p&gt; &lt;p&gt;The file&amp;nbsp;6W41_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze,&amp;nbsp;backmap, and eventually continue the simulations using Amber18 or higher. 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, the&amp;nbsp;file&amp;nbsp;6W41_SIRAHcg_12us_prot.tar&amp;nbsp;contains only the protein coordinates, while&amp;nbsp;6W41_SIRAHcg_12us_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;6W41_SIRAHcg_12us_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 6w41_SIRAHcg_prot.prmtop 6w41_SIRAHcg_prot.ncrst 6w41_SIRAHcg_prot_12us_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 Mart&amp;iacute;n So&amp;ntilde;ora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</dct:description>
    <dct:description>{"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)"]}</dct:description>
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Publication date:
April 30, 2020
DOI:
10.5281/zenodo.3779002

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Keyword(s):
Coronavirus drug design simulation SIRAH coarse-grain CoV2 RBD SARS antibody
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