https://github.com/UranMai/Master-project/wiki

Table of scores for pdb files

Preprocessing PDB file

1. Install Stride from here and copy binary file stride to usr/local/bin
2. Install Phenix from here
3. Run bash preprocess.sh PDBfile

Info about phenix.reduce

Run code

pip install MDAnalysis
pip install igraph

1. Find protein interactions in pdb file, (ex. 1BTL.pdb)

python pdb_class.py file.pdb

2. Calculate energetics and centroid scores

python energetics.py file.pdb
python centroid.py file.pdb

Before using code, pdb file need in preprocessing.

• Add hydrogens using phenix.reduce
• Protonate water using phenix.ready_set
• Make phi file using Stride

Total time	pdb2edge.py	MDA
6vxx.pdb	~3200s	~600s
1BTL.pdb	~40s	~16s
4eiy.pdb	~100s	~30s

PDBFixer

Installation in Colab

pip install -q condacolab

import condacolab
condacolab.install_miniconda()

conda install -y -q -c conda-forge openmm
git clone https://github.com/openmm/pdbfixer.git
python setup.py install