Dataset Open Access

SIRAH-CoV2 initiative: Glycosylated RBD

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

This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike´s RBD glycosylated at Asn331 and Asn343. The initial coordinates correspond to amino acids 327 to 532 taken 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 in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan parameters are available upon request.

The files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and RBD-Man9_SIRAHcg_rawdata_6-10us.tar, contain all 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 files RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar

Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can 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- Untar the file RBD-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 by restype, element, name, etc. 

This dataset is part of the SIRAH-CoV2 initiative.

For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

Files (17.8 GB)
Name Size
RBD-Core-complex_SIRAHcg_glycoprot_10us.tar
md5:ad2b5fdb33bd9c64fa45bdba84277400
680.6 MB Download
RBD-Core-complex_SIRAHcg_glycoprot_10us_skip10ns.tar
md5:da5c9413aed15be21e497776a8656cfb
14.2 MB Download
RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar
md5:e6afef26a068529d5ad35943100ddeaa
5.3 GB Download
RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar
md5:1895649b9e7a7d36bf14dbad450a355f
3.5 GB Download
RBD-Man9_SIRAHcg_glycoprot_10us.tar
md5:95a4f703effde3cbcad047e66dd4c6f6
701.0 MB Download
RBD-Man9_SIRAHcg_glycoprot_10us_skip10ns.tar
md5:cf5fb9ca22f49359bd1b80d9df4b73b1
14.6 MB Download
RBD-Man9_SIRAHcg_rawdata_0-6us.tar
md5:b3a71e240e5bd20550efe684c856072e
4.6 GB Download
RBD-Man9_SIRAHcg_rawdata_6-10us.tar
md5:6fe59151e752d25d0b6825a7bce0f8a3
3.0 GB Download
  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)

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

  • Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)

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