Repository containing various scripts to predict the binding affinity of protein-protein complexes from structure

These scripts allow to calculate properties such as inter-residue distances (ICs) and non-interacting surface properties (NIC) in protein-protein complexes. Such values can be combined with specific weights to predict the binding affinity of the protein complex.

#Usage: ICs: Copy ICs-parameters.sh, icsdistance.py and filter_property.py in the same directory. Launch the program as:

     ./ICs-parameters.sh <pdb-file>
      Example: ./ICs-parameter.sh 2OOB.pdb

NIS: Launch the program as:

 ./parameter_0.5.sh <pdb-file>

Please note that the complex has to contain only TWO interacting chains, labelled as A and B.

ICs_parameters.sh requires python 2.7 version.

NISparameters_0.5.sh requires naccess to be installed. See:www.bioinf.manchester.ac.uk/naccess.

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• If ICs calcualtion scripts package was useful to your research, please cite us

Anna Vangone and Alexandre M.J.J. Bonvin: Contacts-based prediction of binding affinity in protein-protein complexes. eLife 4, e07454 (2015).

• If NIS calculation script was useful to your research, please cite us

Panagiotis L. Kastritis , João P.G.L.M. Rodrigues, Gert E. Folkers, Rolf Boelens, Alexandre M.J.J. Bonvin: Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface. Journal of Molecular Biology, 14, 2632–2652 (2014).

Apache Licence 2.0