SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile
This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the single mutant D614G, and the double mutant T307I/D614G. Simulations are based on the PDB structure 6XR8. Loops were comple...
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Online Access: | https://dx.doi.org/10.5281/zenodo.4725930 https://zenodo.org/record/4725930 |
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ftdatacite:10.5281/zenodo.4725930 2023-05-15T13:54:02+02:00 SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile González-Puelma, Jorge Aldridge, Jacqueline Montes de Oca, Marco Pinto, Mónica Uribe-Paredes, Roberto Fernández-Goycoolea, José Alvarez Saravia, Diego Álvarez, Hermy Encina, Gonzalo Weitzel, Thomas Muñoz, Rodrigo Olivera-Nappa, Álvaro Pantano, Sergio Navarrete, Marcelo A. 2021 https://dx.doi.org/10.5281/zenodo.4725930 https://zenodo.org/record/4725930 en eng Zenodo https://dx.doi.org/10.5281/zenodo.4725931 https://dx.doi.org/10.5281/zenodo.4730896 Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess CC-BY SARS-CoV2 Variants Covid-19 Coarse-Grained Simulation Chile sub-Antarctic dataset Dataset 2021 ftdatacite https://doi.org/10.5281/zenodo.4725930 https://doi.org/10.5281/zenodo.4725931 https://doi.org/10.5281/zenodo.4730896 2021-11-05T12:55:41Z This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the single mutant D614G, and the double mutant T307I/D614G. Simulations are based on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & 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 containing 10 microseconds of the CG protein recorded every 200 picoseconds (50000 frames) iii) a smaller .xtc file containing the same trajectory but with only one frame per nanosecond (1000 frames) iv) a .gro file with the initial configuration Finally, the file sirah_vmdtk.tcl contains a series of macros and scripts that facilitate the visualization and analysis of the CG trajectories. Step-By-Step tutorials for visualizing and analyzing CG trajectories using SirahTools can 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.gro SpikeWT-SIRAH-1kfrm.xtc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative 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 contact Sergio Pantano (spantano@pasteur.edu.uy). Dataset Antarc* Antarctic DataCite Metadata Store (German National Library of Science and Technology) Antarctic Pasteur ENVELOPE(140.099,140.099,-66.625,-66.625) Sever ENVELOPE(166.083,166.083,62.917,62.917) Garay ENVELOPE(-66.968,-66.968,-67.703,-67.703) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
SARS-CoV2 Variants Covid-19 Coarse-Grained Simulation Chile sub-Antarctic |
spellingShingle |
SARS-CoV2 Variants Covid-19 Coarse-Grained Simulation Chile sub-Antarctic González-Puelma, Jorge Aldridge, Jacqueline Montes de Oca, Marco Pinto, Mónica Uribe-Paredes, Roberto Fernández-Goycoolea, José Alvarez Saravia, Diego Álvarez, Hermy Encina, Gonzalo Weitzel, Thomas Muñoz, Rodrigo Olivera-Nappa, Álvaro Pantano, Sergio Navarrete, Marcelo A. SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
topic_facet |
SARS-CoV2 Variants Covid-19 Coarse-Grained Simulation Chile sub-Antarctic |
description |
This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the single mutant D614G, and the double mutant T307I/D614G. Simulations are based on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & 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 containing 10 microseconds of the CG protein recorded every 200 picoseconds (50000 frames) iii) a smaller .xtc file containing the same trajectory but with only one frame per nanosecond (1000 frames) iv) a .gro file with the initial configuration Finally, the file sirah_vmdtk.tcl contains a series of macros and scripts that facilitate the visualization and analysis of the CG trajectories. Step-By-Step tutorials for visualizing and analyzing CG trajectories using SirahTools can 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.gro SpikeWT-SIRAH-1kfrm.xtc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative 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 contact Sergio Pantano (spantano@pasteur.edu.uy). |
format |
Dataset |
author |
González-Puelma, Jorge Aldridge, Jacqueline Montes de Oca, Marco Pinto, Mónica Uribe-Paredes, Roberto Fernández-Goycoolea, José Alvarez Saravia, Diego Álvarez, Hermy Encina, Gonzalo Weitzel, Thomas Muñoz, Rodrigo Olivera-Nappa, Álvaro Pantano, Sergio Navarrete, Marcelo A. |
author_facet |
González-Puelma, Jorge Aldridge, Jacqueline Montes de Oca, Marco Pinto, Mónica Uribe-Paredes, Roberto Fernández-Goycoolea, José Alvarez Saravia, Diego Álvarez, Hermy Encina, Gonzalo Weitzel, Thomas Muñoz, Rodrigo Olivera-Nappa, Álvaro Pantano, Sergio Navarrete, Marcelo A. |
author_sort |
González-Puelma, Jorge |
title |
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
title_short |
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
title_full |
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
title_fullStr |
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
title_full_unstemmed |
SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile |
title_sort |
sirah-cov2 initiative: t307i mutation in a sars-cov-2 spike from sub-antarctic chile |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://dx.doi.org/10.5281/zenodo.4725930 https://zenodo.org/record/4725930 |
long_lat |
ENVELOPE(140.099,140.099,-66.625,-66.625) ENVELOPE(166.083,166.083,62.917,62.917) ENVELOPE(-66.968,-66.968,-67.703,-67.703) |
geographic |
Antarctic Pasteur Sever Garay |
geographic_facet |
Antarctic Pasteur Sever Garay |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
https://dx.doi.org/10.5281/zenodo.4725931 https://dx.doi.org/10.5281/zenodo.4730896 |
op_rights |
Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.5281/zenodo.4725930 https://doi.org/10.5281/zenodo.4725931 https://doi.org/10.5281/zenodo.4730896 |
_version_ |
1766259526295617536 |