Dataset Open Access

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

Exequiel Barrera; Pablo Garay; Florencia Klein; Matías Machado; Martín Soñora; Sergio Pantano

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Endoribonuclease NSP15 in its APO form (PDB id: 6W01, Bioassembly 1). 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 in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020

The file 6W01_SIRAHcg_rawdata.tar contains 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 contains only the protein coordinates, while 6W01_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W01_SIRAHcg_10us_prot_skip10ns.tar

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

vmd 6W01_SIRAHcg_prot.prmtop 6W01_SIRAHcg_prot_10us_skip10ns.ncrst 6W01_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 Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

Files (25.0 GB)
Name Size
6W01_SIRAHcg_10us_prot.tar
md5:1b1bce1bed2c8c7a778a4b4941a2f1b0
6.1 GB Download
6W01_SIRAHcg_10us_prot_skip10ns.tar
md5:713641338e305ef212a5810b3dc82c6f
125.8 MB Download
6W01_SIRAHcg_rawdata.tar
md5:08c5e7dcdd16106607df7f90e1fb8b73
18.8 GB Download
  • Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)

  • Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)

  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)

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