The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
Open accessAbstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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The robust prediction results for mutations in loop versus non-loop and mutations with different residue size changes indicate that the short refinement in explicit solvent performed by HADDOCK can handle a small degree of conformational changes and remove steric clashes.
“The robust prediction results for mutations in loop versus non‐loop and mutations with different residue size changes indicates that this approach—the short refinement in explicit solvent performed by HADDOCK—can handle a small degree of conformational changes and remove steric clashes.”
From iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations (2019) · cites this paper as [29]
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- Authors
- van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J.
- Affiliations
- Utrecht University (NL)
- Centre National de la Recherche Scientifique (FR)
- European Molecular Biology Laboratory (DE)
- Hubrecht Institute for Developmental Biology and Stem Cell Research (NL)
- Corresponding author
- Bonvin, A.M.J.J.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2016-02
- Volume
- 428
- Issue
- 4
- Pages
- 720-725
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2154019529
- Cited by
- 2,785
- References
- 25
- Citations by year
- 2026: 149 · 2025: 282 · 2024: 402 · 2023: 413 · 2022: 402 · 2021: 388 · 2020: 309 · 2019: 191 · 2018: 124 · 2017: 90 · 2016: 28 · 2013: 1 · 2012: 1
- FWCI
- 35.39
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by-nc-nd)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- VICI (700.96.442)
- ECHO (711.011.009)
- e-NMR (213010)
- WeNMR (261572)
- EGI-Engage (654142)
- INDIGO-DataCloud (653549)
- 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
- web server, integrative structural biology, biomolecular complexes, quaternary structure prediction, protein-protein docking, drug design
- MeSH terms
- Molecular Biology, Computational Biology, Internet, Macromolecular Substances
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