SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)
DOI10.5281/zenodo.4044378Zenodo4044378MaRDI QIDQ6704839
Dataset published at Zenodo repository.
Sergio Pantano, Florencia Klein, Exequiel Barrera, Martín Soñora, Matías MacHado, Pablo Garay
Publication date: 25 September 2020
Copyright license: Creative Commons Attribution 4.0 International
This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3adimeric transmembrane protein(PDB id: 6XDC, Bioassembly 1) embedded in a membranepatch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion.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 inBarrera et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020. 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 usingSirahToolscan be found at www.sirahff.com. Additionally, 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 containall 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 analyzingCG trajectories usingSirahToolscan be found at www.sirahff.com. Additionally, thefile6XDC_SIRAHcg_10us_prot-memb_skip10ns.tarcontains only the protein and phospholipidscoordinates, withone frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc.,and coloring byrestype, element, name, etc. This dataset is part of the SIRAH-CoV2initiative. For further details, please contact Exequiel Barrera(ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
This page was built for dataset: SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)
