SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)

<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a&nbsp;dimeric transmembrane protein&nbsp;(PDB id: 6XDC, Bioassembly 1) embedded in a membrane&nbsp;patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion.&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&nbsp;<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00435">Barrera et al. JCTC 2019</a>, adding 150 mM NaCl according to&nbsp;<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado &amp; Pantano JCTC 2020</a>.&nbsp;</p> <p>The files 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&nbsp;<a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a>&nbsp;can be found at www.sirahff.com. Additionally, &nbsp;</p> <p>The files 6xdc_SIRAHcg_rawdata_0-2us.tar, 6xdc_SIRAHcg_rawdata_2-4us.tar, 6xdc_SIRAHcg_rawdata_4-6us.tar, 6xdc_SIRAHcg_rawdata_6-8us.tar, and 6xdc_SIRAHcg_rawdata_8-10us.tar contain&nbsp;all the raw information required to visualize (on VMD), analyze,&nbsp;backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing&nbsp;CG trajectories using&nbsp;<a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a>&nbsp;can be found at www.sirahff.com.</p> <p>Additionally, the&nbsp;file&nbsp;6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar&nbsp;contains only the protein and phospholipids&acute;&nbsp;coordinates, with&nbsp;one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc.,&nbsp;and coloring by&nbsp;restype, element, name, etc.&nbsp;</p> <p>This dataset is part of the SIRAH-CoV2&nbsp;initiative.</p> <p>For further details, please contact Exequiel Barrera&nbsp;(ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>