Title: SIRAH-CoV2 initiative: NSP15 Endonuclease (PDB id:6W01)

Type Dataset Exequiel Barrera, Pablo Garay, Florencia Klein, Matías Machado, Martín Soñora, Sergio Pantano (2020): SIRAH-CoV2 initiative: NSP15 Endonuclease (PDB id:6W01). Zenodo. Dataset. https://zenodo.org/record/3742102

Authors: Exequiel Barrera (Institut Pasteur de Montevideo) ; Pablo Garay (Institut Pasteur de Montevideo) ; Florencia Klein (Institut Pasteur de Montevideo) ; Matías Machado (Institut Pasteur de Montevideo) ; Martín Soñora (Institut Pasteur de Montevideo) ; Sergio Pantano (Institut Pasteur de Montevideo) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Endopeptidase NSP15 in its APO form (PDB id: 6W01, Bioassembly 1). 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 Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & 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 using SirahTools can be found at www.sirahff.com. Additionally, the file 6W01_SIRAHcg_10us_prot.tar contain only the protein coordinates, while 6W01_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

This dataset is part of the SIRAH-CoV2 initiative.

For further details, please contact Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

More information

• DOI: 10.5281/zenodo.3742102
• Language: en

Subjects

• Coronavirus, drug design, simulation, SIRAH, coarse-grain, CoV2 Endonuclease, COVID-19, SARS

Dates

• Publication date: 2020
• Issued: April 10, 2020

Notes

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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