HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes

Giulini, M.; Reys, V.; Teixeira, J. M. C.; Jimenez-Garcia, B.; Honorato, R. V.; Kravchenko, A.; Xu, X.; Versini, R.; Engel, A.; Verhoeven, S.; Bonvin, A. M. J. J.

doi:10.1101/2025.04.30.651432

bioRxiv · 10.1101/2025.04.30.651432

HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes

Giulini, M.·Reys, V.·Teixeira, J. M. C.·Jimenez-Garcia, B.·Honorato, R. V.·Kravchenko, A.·Xu, X.·Versini, R.·Engel, A.·Verhoeven, S.·Bonvin, A. M. J. J.

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Abstract

HADDOCK is a widely used resource for integrative modelling of a variety of biomolecular complexes that is able to incorporate experimental knowledge into physics-based calculations during complex prediction, refinement, scoring and analysis. Here we introduce HADDOCK3, the new modular version of the program, in which the original, parameterisable albeit rigid pipeline has been first broken down in a catalogue of independent modules and then enriched with powerful analysis tools and third-party integrations. Thanks to this increased flexibility, HADDOCK3 can now handle multiple integrative modelling scenarios, providing a valuable, physics-based tool to enrich and complement the predictions made by machine learning algorithms in the post-AlphaFold era. We present examples of successful applications of HADDOCK3 that were not feasible with the previous versions of HADDOCK, highlighting its expanded capabilities. The HADDOCK3 software source code is freely available from the GitHub repository (https://github.com/haddocking/haddock3) and comes with an online user guide (www.bonvinlab.org/haddock3-user-manual). All example data described in this manuscript are available at https://github.com/haddocking/haddock3-paper-data.

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Giulini, M., Reys, V., Teixeira, J. M. C., Jimenez-Garcia, B., Honorato, R. V., Kravchenko, A., Xu, X., Versini, R., Engel, A., Verhoeven, S., Bonvin, A. M. J. J.. 2025-05-07. HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes. https://doi.org/10.1101/2025.04.30.651432

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