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@haddocking

HADDOCK

Computational Structural Biology Group @ Utrecht University

Welcome to the BonvinLab GitHub page

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The BonvinLab is a Computational Structural Biology group that focuses on dissecting, understanding and predicting biomolecular interactions at the molecular level. Our research is focused on the development of integrative computational methods for the study of biomolecular interactions, with a particular emphasis on the structural characterization of protein-protein and protein-ligand complexes.

We are part of the Bijvoet Center for Biomolecular Research at Utrecht University, affiliated with the Netherlands eScience Center and one of the core applications of the BioExcel Center of Excellence for Computational Biomolecular Research under EuroHPC.

Featured research software

  • haddock3: The High Ambiguity Driven biomolecular DOCKing is our flagship software, it is an integrative platform for modelling biomolecular complexes. It is one of the most popular software for protein-protein and protein-ligand docking.
  • pdb-tools: A dependency-free cross-platform swiss army knife for PDB files.
  • prodigy: Predict the binding affinity of protein-protein complexes from structural data
  • arctic3d: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
  • proabc-2: Deep learning framework to predict antibody paratope residues
  • disvis: Visualisation of conformational space restriction by distance restraints

Useful utilities

  • haddock-restraints: Generate restraints to be used in HADDOCK
  • haddock-runner: Run large scale HADDOCK simulations using multiple input molecules in different scenarios
  • haddock-tools: Set of useful utility scripts developed by the BonvinLab group members
  • haddock-mmcif: Encode information from a HADDOCK run to a cif file to be deposited in PDB-Dev

Contact

If you would like to get in touch with us, please send an email to bonvinlab.support@uu.nl

Pinned Loading

  1. haddock3 haddock3 Public

    Official repo of the modular BioExcel version of HADDOCK

    Python 119 40

  2. arctic3d arctic3d Public

    Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

    Python 28 6

  3. pdb-tools pdb-tools Public

    A dependency-free cross-platform swiss army knife for PDB files.

    Python 391 114

  4. prodigy prodigy Public

    Predict the binding affinity of protein-protein complexes from structural data

    Python 114 27

  5. haddock-runner haddock-runner Public

    Run large scale HADDOCK simulations using multiple input molecules in different scenarios

    Go 3 1

  6. haddock-restraints haddock-restraints Public

    Generate restraints to be used in HADDOCK

    Rust 2 1

Repositories

Showing 10 of 62 repositories
  • haddock3 Public

    Official repo of the modular BioExcel version of HADDOCK

    haddocking/haddock3’s past year of commit activity
    Python 119 Apache-2.0 40 13 9 Updated Dec 12, 2024
  • haddocking.github.io Public

    Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

    haddocking/haddocking.github.io’s past year of commit activity
    HTML 13 MIT 21 1 4 Updated Dec 11, 2024
  • fandas Public

    Repository of the FANDAS code for prediction ssNMR spectra from structure

    haddocking/fandas’s past year of commit activity
    Python 2 Apache-2.0 0 5 2 Updated Dec 9, 2024
  • haddock-restraints Public

    Generate restraints to be used in HADDOCK

    haddocking/haddock-restraints’s past year of commit activity
    Rust 2 MIT 1 0 1 Updated Dec 9, 2024
  • haddock-runner Public

    Run large scale HADDOCK simulations using multiple input molecules in different scenarios

    haddocking/haddock-runner’s past year of commit activity
    Go 3 Apache-2.0 1 0 0 Updated Dec 9, 2024
  • arctic3d Public

    Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

    haddocking/arctic3d’s past year of commit activity
    Python 28 Apache-2.0 6 4 5 Updated Dec 5, 2024
  • haddocking/protein-glycans’s past year of commit activity
    Python 3 Apache-2.0 0 0 0 Updated Dec 4, 2024
  • cport Public

    CPORT is a Consensus Prediction Of interface Residues in Transient complexes used to predict protein-protein interface residues.

    haddocking/cport’s past year of commit activity
    Python 2 Apache-2.0 3 5 3 Updated Dec 2, 2024
  • .github Public
    haddocking/.github’s past year of commit activity
    0 0 0 0 Updated Nov 28, 2024
  • powerfit Public

    Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

    haddocking/powerfit’s past year of commit activity
    Python 20 Apache-2.0 7 4 0 Updated Nov 19, 2024