This code contains a collection of python scripts for calculating structural properties of protein complexes.

Install

Download the code and run

python setup.py install

How to execute the script

1. Create a text file with the proteins of interest and the interacting chains where the ":" symbol indicates the protein-protein interface that is being investigated. For example:

1AKJ_AB:DE
1AK4_A:D

2. Invoke setupPpiDb.py on the file you just created. For example (assuming it is saved as PDBs.txt):

python setupPpiDb.py PDBs.txt

Follow the script instructions and that's it!

PPI features

The above script will:

• Download PDBs from the RCSB PDB
• Add hydrogens using molprobity
• Calculate/identify the following properties:
  • Accessible surface area (ASA)
  • interface atoms/residues in the molecule (ΔASA > 0 or Distance > 4)
  • periphery index
  • hydrogen bonds
  • Van der Waals
  • Electrostatic charges
• All the results are saved to csv files and to SQL database

Credits

All the scripts were developed in Dr. Julia Shifman lab.

1. Erijman, Ariel, Eran Rosenthal, and Julia Shifman, How Structure Defines Affinity in Protein-Protein Interactions. PLOS one 9.10 (2014)