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Multiscale CG Models for the SARS-CoV-2 Virion

This repository contains coarse-grained (CG) models for the SARS-CoV-2 virion developed in response to the COVID-19 pandemic.

Image of virion

If using these models, please cite:
https://pubmed.ncbi.nlm.nih.gov/33253634/

Please note that these are currently under development.

Files Description References
S-trimer-cg.pdb CG model of the S protein trimer
M-dimer-cg.pdb CG model of the M protein dimer
E-pentamer-cg.pdb CG model of the E protein pentamer
lipid-cg.pdb CG lipid model arXiv:1910.05362
S-timer-aa.pdb All-atom model of the S protein trimer https://doi.org/10.1021/acscentsci.0c01056
M-dimer-aa.pdb All-atom model of the M protein dimer https://doi.org/10.1101/2020.03.25.008904
E-pentamer-aa.pdb All-atom model of the E protein pentamer https://dx.doi.org/10.3390%2Fv12040360
lipid-aa.pdb All-atom model of a POPC lipid patch
cg-virion.pdb CG model of the SARS-CoV-2 virion
cg-virion.data LAMMPS data file for the CG virion
cg-virion.ff Force-field parameters for the CG virion
cg-virion.psf CG PSF file for the virion
cg-virion.dcd Subsampled DCD trajectory for the virion

Department of Chemistry
University of Chicago

Contact:
yua@uchicago.edu

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