Alexandre Bonvin bio photo

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

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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