SIRAH-CoV2 initiative: Glycosylated RBD
SIRAH-CoV2 initiative: Glycosylated RBD (Dataset published at Zenodo repository.)
DOI10.5281/zenodo.3903522Zenodo3903522MaRDI QIDQ6704836
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 22 June 2020
Copyright license: No records found.
This dataset contains the trajectories of10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spikes RBD glycosylated at Asn331and Asn343. The initial coordinates correspond to amino acids 327 to 532taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI (http://www.charmm-gui.org). There are two different sets of simulations corresponding to Core Complex and High Mannose. 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. Glycan parametersare available upon request. The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar andRBD-Man9_SIRAHcg_rawdata_6-10us.tar,containall the raw information required to visualize (on VMD), analyze, and backmap the simulations of High Mannose glycosylated RBD. Analogous information for Core-complex glycosylations is contained in filesRBD-Core-complex_SIRAHcg_rawdata_0-6us.tar andRBD-Core-complex_SIRAHcg_rawdata_6-10us.tar Step-By-Step tutorials for running, visualizing, and analyzingCG trajectories usingSirahToolscan be found at www.sirahff.com. Additionally, files with names ending in SIRAHcg_10us_glycoprot.tar contain only the protein coordinates, while file names ending with SIRAHcg_10us_glycoprot_skip10ns.tar contains one frame every 10ns. To take a quick look at a trajectory: 1- Untarthe fileRBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd glyco-RBD_SIRAHcg_glycoprot.prmtop glyco-RBD_SIRAHcg_glycoprot.ncrst glyco-RBD_SIRAHcg_glycoprot_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 Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
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