README.md

Computational Analysis of Dynamic Allostery and Control in the SARS-CoV-2 Main Protease

Processed data and figure generation codes for a project on an Elastic Network Model analysis of the SARS-CoV-2 main protease (M^pro, aka 3CL^pro). See preprint in bioRxiv.

PDB

We used 6LU7 X-ray crystallographic structure of the main protease to construct apo (ligand-free), holo1 (one ligand present) and holo2 protein forms (two ligands present, native form).

Software

All ENM's data was generated and processed via Durham Dynamic Protein Toolbox, 'DDPT' for short, an open-source FORTRAN based protein analysis toolbox.

Visualization

Python scripts were used for the processed data visualization.

Data

This work presents four types of data:

1. Wild-type ENM Gibbs free energies
2. Cross-correlation of motion
3. 1-point mutational scans.
4. 2-point mutational scans.