#Binding Affinity Prediction Tools Collection of scripts to calculate predictive indexes of binding affinity values for protein-protein complexes from atomic structures.
The scripts implement several binding affinity predictors:
#Quick & Dirty Installation
git clone http://github.com/biopython/biopython.git
cd biopython
sudo python setup.py install # Alternatively, install locally but fix $PYTHONPATH
wget http://freesasa.github.io/freesasa-1.0.tar.gz
tar -xzvf freesasa-1.0.tar.gz
cd freesasa-1.0
./configure && make && make install
git clone http://github.com/haddocking/binding_affinity
# Edit the config.py to setup the paths to the freesasa binary and radii files
# Have fun!#Usage
- Non-Interacting Surface (NIS) model
python predict_NIS.py <pdb file>- Contacts-based model
python predict_IC.py <pdb file>#Installation & Dependencies The scripts rely on Biopython to validate the PDB structures and calculate interatomic distances. freesasa, with the parameter set used in NACCESS (Chothia, 1976), is also required for calculating the buried surface area.
DISCLAIMER: given the different software to calculate solvent accessiblity, predicted values might differ (very slightly) from those published in the reference implementations. The correlation of the actual atomic accessibilities is over 0.99, so we expect these differences to be very minor.
To install and use the scripts, just clone the git repository or download the tarball zip
archive. Make sure freesasa and Biopython are accessible to the Python scripts
through the appropriate environment variables ($PYTHONPATH).
#License These utilities are open-source and licensed under the Apache License 2.0. For more information read the LICENSE file.
#Citing us If any of the predictive models or scripts are useful to you, consider citing them in your publications:
Anna Vangone and Alexandre M.J.J. Bonvin: Contacts-based prediction of binding affinity in protein-protein complexes. Revision in eLife (2015) (link)
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). (link)