Title: SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF)

Type Dataset Martín Soñora, Exequiel Barrera, Pablo Garay, Florencia Klein, Matías Machado, Sergio Pantano (2020): SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF). Zenodo. Dataset. https://zenodo.org/record/3865479

Authors: Martín Soñora (Institut Pasteur de Montevideo) ; Exequiel Barrera (Institut Pasteur de Montevideo) ; Pablo Garay (Institut Pasteur de Montevideo) ; Florencia Klein (Institut Pasteur de Montevideo) ; Matías Machado (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 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). 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. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 7BTF_SIRAHcg_rawdata_0-2us.tar,  7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar, 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 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD 1.9.3 using the command line:

vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -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 further details, please contact Martin Soñora (msonora@pasteur.edu.uy) Sergio Pantano (spantano@pasteur.edu.uy).

More information

• DOI: 10.5281/zenodo.3865479
• Language: en

Subjects

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

Dates

• Publication date: 2020
• Issued: May 29, 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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