10.5281/zenodo.3779002
https://zenodo.org/records/3779002
oai:zenodo.org:3779002
Martín Soñora
Martín Soñora
0000-0003-3872-6117
Institut Pasteur de Montevideo
Exequiel Barrera
Exequiel Barrera
0000-0002-0388-3078
Institut Pasteur de Montevideo
Pablo Garay
Pablo Garay
0000-0001-6604-0329
Institut Pasteur de Montevideo
Florencia Klein
Florencia Klein
0000-0003-4099-9907
Institut Pasteur de Montevideo
Matías Machado
Matías Machado
0000-0002-9971-4710
Institut Pasteur de Montevideo
Sergio Pantano
Sergio Pantano
0000-0001-6435-4543
Institut Pasteur de Montevideo
SIRAH-CoV2 initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41)
Zenodo
2020
Coronavirus
drug design
simulation
SIRAH
coarse-grain
CoV2 RBD
SARS
antibody
2020-04-30
eng
10.5281/zenodo.3779001
https://zenodo.org/communities/covid-19
SIRAH version 2.2, Amber18
Creative Commons Attribution 4.0 International
This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41). 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. Glycans have been removed from the structures.
The file 6W41_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 6W41_SIRAHcg_12us_prot.tar contains only the protein coordinates, while 6W41_SIRAHcg_12us_prot_skip10ns.tar contains one frame every 10ns.
To take a quick look at the trajectory:
1- Untar the file 6W41_SIRAHcg_12us_prot_skip10ns.tar
2- Open the trajectory on VMD using the command line:
vmd 6w41_SIRAHcg_prot.prmtop 6w41_SIRAHcg_prot.ncrst 6w41_SIRAHcg_prot_12us_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 Martín Soñora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).