HADDOCK3

High Ambiguity Driven biomolecular DOCKing.

Version: 2025.5.0

Authors: Computational structural biology group, Utrecht University

Contact:

Bijvoet Center for Biomolecular Research
Padualaan 8, 3584 CH Utrecht, the Netherlands
Email: a.m.j.j.bonvin@uu.nl
Phone: +31-30-2532652

HADDOCK is one of the flagship software in the EU H2020 BioExcel Center of Excellence for Biomolecular Research

Publication:

M. Giulini#, V. Reys#, J.M.C. Teixeira, B. Jiménez-García, R.V. Honorato, A. Kravchenko, X. Xu, R. Versini, A. Engel, S. Verhoevenand A.M.J.J. Bonvin. HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes. BioRXiv. 10.1101/2025.04.30.651432 (2025).

Description

HADDOCK v3.0 is a bottom-up reimagination of the long standing time-proven HADDOCK used for integrative modeling of biomolecular complexes. This young and still very experimental (use it at your own risk!) aims to modularize and extend HADDOCK’s core functions.

In its current implementation, HADDOCK v3.0 still lacks the full repertoire of features present at the production web server version, HADDOCK v2.4. However it is able to take full advantage of the ambiguous interaction restraints (AIRs) to drive the docking process.

Manuals

HADDOCK3 documentation (for developers) Documentation for HADDOCK3 including installation instructions.
HADDOCK3 user manual User manual for HADDOCK3, with a comprehensive description of the software and its features, including a Best Practices section and descriptions of several HADDOCK docking scenarios.
HADDOCK restraints generation: A guide for the haddock-restraints tool allowing to generate various types of distance restraints for use in HADDOCK.

HADDOCK3 distribution download

HADDOCK v3.0 can be freely downloaded by completing the following form (see our privacy statement regarding the use of our portals):

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