HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes
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Abstract
HADDOCK is a widely used resource for integrative modeling 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, parametrizable albeit rigid pipeline has been first broken down into 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 modeling 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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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Accurate structure prediction of biomolecular interactions with AlphaFold 3
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Evolutionary-scale prediction of atomic level protein structure with a language model
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
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Self-citationImproved prediction of protein-protein interactions using AlphaFold2
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- Authors
- Giulini, M., Reys, V., Teixeira, J. M. C., Jiménez-García, B., V. Honorato, R., 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
- American Chemical Society (ACS)
- Published
- 2025-06-17
- Volume
- 65
- Issue
- 13
- Pages
- 7315-7324
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC12264957
- OpenAlex
- W4411370561
- Cited by
- 51
- References
- 8
- Citations by year
- 2026: 39 · 2025: 11 · 2024: 1
- FWCI
- 15.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- 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
- European High Performance Computing Joint Undertaking (BioExcel / 101093290)
- HORIZON EUROPE European Innovation Council (BioExcel / 823830)
- Netherlands eScience Center (027.020.G13)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › 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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