SIRAH-CoV2 initiative: Spike D614G mutation (introduced on PDB id:6XR8)
DOI10.5281/zenodo.4311516Zenodo4311516MaRDI QIDQ6704843
Dataset published at Zenodo repository.
Matías MacHado, Martín Soñora, Sergio Pantano, Pablo Garay, Exequiel Barrera, Florencia Klein
Publication date: 8 December 2020
Copyright license: Creative Commons Attribution 4.0 International
This dataset contains the raw data of a coarse-grained molecular dynamics simulation of the D614G mutant ofSpikeproteinfromSARS-CoV-2. The initial coordinates correspond to the PDB structure 6XR8, where the coordinates of the side chain of Aspartate614 were deleted to produce aGlycine. Missing loops were introduced with Swiss-Model (https://swissmodel.expasy.org).Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported inMachado et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020.Glycan parameters correspond to those reported byGaray et at.2020. The files spike_D614G_SIRAHcg_rawdata_0-2us.tar, spike_D614G_SIRAHcg_rawdata_2-4us.tar,spike_D614G_SIRAHcg_rawdata_4-6us.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, thefilespike_D614G_SIRAHcg_prot_10us.tarcontains only the protein coordinates, whilespike_D614G_SIRAHcg_prot_10us_skip10ns.tar contains one frame every 10ns. Notice that these two files contain a 10-microsecond trajectory, while the raw data is limited to 6 microseconds because of size restrictions on the database. Raw data from microseconds 6 to 10 is available upon request (see below). To take a quick look at the trajectory: 1- Untarthe filespike_D614G_SIRAHcg_prot_10us_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd spike_D614G_SIRAHcg_prot.prmtopspike_D614G_SIRAHcg_prot.ncrstspike_D614G_SIRAHcg_10us_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-CoV-2initiative. For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
This page was built for dataset: SIRAH-CoV2 initiative: Spike D614G mutation (introduced on PDB id:6XR8)
