This is collection of simple python scripts for calculating basic structural properties/features of protein complexes.

Install

Download the code and run

python setup.py install

Usage

You can either use the scripts directly or use master script setupPpiDb to run most of them on a list of proteins.

For basic usage:

1. Create a text file with list of proteins and the interacting chains, 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](http://molprobity.biochem.duke.edu/)
* Calculate various properties:
* Accessible surface area ([ASA](https://en.wikipedia.org/wiki/Accessible_surface_area))
* 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](http://bio.huji.ac.il/shifman/index.html).

1. Erijman, Ariel, Eran Rosenthal, and Julia Shifman, [How Structure Defines Affinity in Protein-Protein Interactions](http://dx.doi.org/10.1371/journal.pone.0110085). PLOS one 9.10 (2014)