3766270
doi
10.5281/zenodo.3766270
oai:zenodo.org:3766270
user-covid-19
Exequiel Barrera
Institut Pasteur de Montevideo
Pablo Garay
Institut Pasteur de Montevideo
Matías Machado
Institut Pasteur de Montevideo
Martín Soñora
Institut Pasteur de Montevideo
Sergio Pantano
Institut Pasteur de Montevideo
SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)
Florencia Klein
Institut Pasteur de Montevideo
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 Papain-like Protease
COVID-19
SARS
Molecular Dynamics
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C). 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>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p>
<p>The files 6W9C_SIRAHcg_rawdata_0-5us.tar, 6W9C_SIRAHcg_rawdata_5-10us.tar, contain 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 6W9C_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W9C_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 6W9C_SIRAHcg_10us_prot_skip10ns.tar</p>
<p>2- Open the trajectory on VMD using the command line:</p>
<p>vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst 6W9C_SIRAHcg_10us_prot_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 Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Zenodo
2020-04-25
info:eu-repo/semantics/other
3766269
user-covid-19
SIRAH version 2.2, Amber18
1610557307.492757
6458306560
md5:ae03ef7d4783b1d281b67bf0cc15c787
https://zenodo.org/records/3766270/files/6W9C_SIRAHcg_rawdata_0-5us.tar
2748334080
md5:279018f8f05f1082b5fcae203c3fe611
https://zenodo.org/records/3766270/files/6W9C_SIRAHcg_10us_prot.tar
6458306560
md5:6838bcd6b6374bdeb7a8a30076791a8d
https://zenodo.org/records/3766270/files/6W9C_SIRAHcg_rawdata_5-10us.tar
56862720
md5:13aa7e3687ab4e3be9566e6ca660fe94
https://zenodo.org/records/3766270/files/6W9C_SIRAHcg_10us_prot_skip10ns.tar
public
10.5281/zenodo.3766269
isVersionOf
doi