Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

Email Github Youtube Subscribe

This page provide you links to software and software manuals of the computational structural biology group.



  • HADDOCKING GitHub repository

    The GitHub repository for HADDOCK and its associated tools

    • Binding_affinity: PRODIGY: A collection of Python scripts to predict the binding affinity in protein-protein complexes.

    • DisVis: A Python package and command-line tool to quantify and visualize the accessible interaction space of distance-restrained biomolecular complexes.

    • Fraction of common contact clustering: Clustering of biomolecular complexes based on the fraction of common contacts

    • HADDOCK-tools: A collection of useful scripts related to HADDOCK

    • PDB-tools: A collection of Python scripts for the manipulation (renumbering, changing chain and segIDs…) of PDB files

    • PowerFit: PowerFit is a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.

    • Samplex: Samplex is an automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). Samplex takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state.


  • 3D-DART DNA modelling

    3D-DART provides a convenient means of generating custom structural models of DNA.



  • Bioinformatics interface predictors

    • WHISCY WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information.

    • CPORT CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor