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.
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