SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile (Dataset published at Zenodo repository.)
DOI10.5281/zenodo.4730896Zenodo4730896MaRDI QIDQ6704857
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 28 April 2021
Copyright license: No records found.
This dataset contains the trajectoriesof10microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, thesingle mutant D614G, and the double mutant T307I/D614G. Simulations are basedon the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations wereperformed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideounder the conditions reported inMachado et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020. The following files in gromacs format are provided for each simulation: i) a .psf containing the topological information (connectivity, etc) ii) a big.xtc file containing10 microseconds of the CG proteinrecorded every 200 picoseconds(50000 frames) iii) a smaller .xtc file containingthe same trajectory but with only one frame per nanosecond(1000 frames) iv) a .gro file with the initial configuration Finally, the filesirah_vmdtk.tcl contains a series of macros and scripts that facilitatethe visualization andanalysis of the CG trajectories.Step-By-Step tutorials forvisualizing and analyzingCG trajectories usingSirahToolscan be found at www.sirahff.com. To take a quick look at a trajectory using VMD 1.9.3, run the command: vmd SpikeWT-SIRAH.psf SpikeWT-SIRAH.groSpikeWT-SIRAH-1kfrm.xtc -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 data sharing. If you use this data, please cite Garay PG, et al The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations Dataset of the SARS-CoV-2 Proteome. Front. Med. Technol. 3:644039. doi: 10.3389/fmedt.2021.644039 For further details, please contactSergio Pantano (spantano@pasteur.edu.uy).
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