/covid

Druggability analysis of SARS-CoV-2

Project Status: Active – The project has reached a stable, usable state and is being actively developed.

covid

Druggability analysis of SARS-CoV-2

We examine pockets on the experimentally determined and modelled proteome of SARS-CoV-2. We extend this to look for binding pockets that arise from complex formation and pockets that can be targeted to disrupt protein-protein interactions.

Requirements

  1. fPocket Linux install:
git clone https://github.com/Discngine/fpocket.git
cd fpocket
make 
sudo make install
  1. EBI PISA

Data

  1. Structures experimental_structures - Experimental Structures collected from PDB

korkin_lab/IndividualModels korkin_lab/IntraViralComplexes korkin_lab/ViralHumanComplexes Collected from Korkin Lab

deepmind_structures - Models produced by AlphaFold

AlphaFold_refined - Alphafold models refined by Feig Lab

FeigLab - Models produced by Feig Lab

  1. Pockets

Same directory structure as above. Pockets generated by fPocket. Pocket scores parsed by parse_pocket_scores.ipynb to produce the score index files in /pockets/

  1. Interfaces

Produced from models using EBI PISA