Martín Soñora
Exequiel Barrera
Pablo Garay
Florencia Klein
Matías Machado
Sergio Pantano
2020-04-16
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 NSP9 RNA binding protein (PDB id: 6W4B, Bioassembly 1). 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 <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p>
<p>The file 6W4B_SIRAHcg_rawdata.tar 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 <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p>
<p>Additionally, the file 6W4B_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W4B_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p>
<p>To take a quick look at the trajectory:</p>
<p>1- Untar the file 6W4B_SIRAHcg_10us_prot_skip10ns.tar</p>
<p>2- Open the trajectory on VMD using the command line:</p>
<p>vmd 6W4B_SIRAHcg_prot.prmtop 6W4B_SIRAHcg_prot.ncrst 6W4B_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p>
<p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p>
<p>This dataset is part of the SIRAH-CoV2 initiative.</p>
<p>For further details, please contact Sergio Pantano (spantano@pasteur.edu.uy).</p>
https://doi.org/10.5281/zenodo.3754643
oai:zenodo.org:3754643
eng
Zenodo
https://zenodo.org/communities/covid-19
https://doi.org/10.5281/zenodo.3754642
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Coronavirus
drug design
simulation
SIRAH
coarse-grain
CoV2 NSP9
COVID-19
SARS
SIRAH-CoV2 initiative: NSP9 RNA binding protein (PDBid:6W4B)
info:eu-repo/semantics/other