SIRAH-CoV2 initiative: RNA binding domain of nucleocapsid phosphoprotein (PDB id:6VYO)
DOI10.5281/zenodo.3747621Zenodo3747621MaRDI QIDQ6704819
Dataset published at Zenodo repository.
Exequiel Barrera, Matías MacHado, Pablo Garay, Martín Soñora, Florencia Klein, Sergio Pantano
Publication date: 10 April 2020
Copyright license: Creative Commons Attribution 4.0 International
This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA binding domain of the nucleocapsid phosphoprotein in its APO form with Zn ions bound (PDB id:6VYO, 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 inMachado et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020. Zinc ions were parameterized as reported inKlein et al. 2020. The file6VYO_SIRAHcg_rawdata.tarcontains 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 usingSirahToolscan be found at www.sirahff.com.Additionally, thefile6VYO_SIRAHcg_10us_prot.tarcontains only the protein coordinates, while6VYO_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6VYO_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd6VYO_SIRAHcg_prot_10us_skip10ns.prmtop 6VYO_SIRAHcg_prot_10us_skip10ns.ncrst 6VYO_SIRAHcg_prot_10us_skip10ns.nc -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 further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
This page was built for dataset: SIRAH-CoV2 initiative: RNA binding domain of nucleocapsid phosphoprotein (PDB id:6VYO)
