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HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes
Open accessPreprint — published as 10.1021/acs.jcim.5c00969 · Paper page
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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Metadata
- Authors
- Giulini, M., Reys, V., Teixeira, J. M. C., Jiménez-García, B., Honorato, R. V., Kravchenko, A., Xu, X., Versini, R., Engel, A., Verhoeven, S., & Bonvin, A. M. J. J.
- Affiliations
- Utrecht University (NL)
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands eScience Center (NL)
- Corresponding author
- Bonvin, Alexandre M.J.J.
- ORCID
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- openRxiv
- Published
- 2025-05-07
- Volume
- 65
- Issue
- 13
- Pages
- 7315-7324
- ISSN
- 1549-9596 (ISSN-L)
- PMC
- PMC12264957
- OpenAlex
- W4411370561
- Cited by
- 51
- References
- 44
- Citations by year
- 2026: 39 · 2025: 11
- FWCI
- 15.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Horizon Europe (BioExcel 823830)
- European High Performance Computing Joint Undertaking (BioExcel 101093290)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- HADDOCK3, integrative modeling, biomolecular complexes, protein-protein interaction, docking, refinement, scoring
- MeSH terms
- Models, Molecular, Proteins, Software
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