Encyclopedia of Biophysics

2013 Edition
| Editors: Gordon C. K. Roberts

HADDOCK

  • Alexandre M. J. J. BonvinEmail author
  • M. van Dijk
  • E. Karaca
  • P. L. Kastritis
  • Adrien S. J. Melquiond
  • C. Schmitz
  • S. J. de Vries
Reference work entry
DOI: https://doi.org/10.1007/978-3-642-16712-6_330

Definition

HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes (Dominguez et al. 2003). Docking is defined as the modeling of the structure of a complex based on the known three-dimensional structures of its constituents. HADDOCK distinguishes itself from other docking methods by incorporating a wide variety of experimental and/or bioinformatics data to drive the modeling (Melquiond and Bonvin 2010). This allows concentrating the search to relevant portions of the interaction space using a more sophisticated treatment of conformational flexibility.

Interface regions can be identified by mutagenesis,  H/D exchange, and chemical modifications (e.g., by cross-linkers or oxidative agents) detected by  mass spectrometry,  nuclear magnetic resonance, chemical shift perturbations, and cross-saturation transfer. When experimental data are unavailable or scarce, this information can be supplemented...

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References

  1. de Vries SJ, Bonvin AMJJ. How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Prot & Pept Sci. 2008;9:394–406.PubMedGoogle Scholar
  2. de Vries SJ, van Dijk M, Bonvin AMJJ. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010;5:883–97.PubMedGoogle Scholar
  3. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003;125:1731–7.PubMedGoogle Scholar
  4. Melquiond ASJ, Bonvin AMJJ. Data-driven docking: using external information to spark the biomolecular rendez-vous. In: Zacharias M, editor. Protein-protein complexes: analysis, modeling and drug design. London: Imperial College; 2010. p. 183–209.Google Scholar
  5. Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ. Next challenges in protein-protein docking: from proteome to interactome and beyond. Wiley Interdisciplinary Reviews: Computational Molecular Science. 2011; Early View doi: 10.1002/wcms.91Google Scholar

Copyright information

© European Biophysical Societies' Association (EBSA) 2013

Authors and Affiliations

  • Alexandre M. J. J. Bonvin
    • 1
    Email author
  • M. van Dijk
    • 1
  • E. Karaca
    • 1
  • P. L. Kastritis
    • 1
  • Adrien S. J. Melquiond
    • 1
  • C. Schmitz
    • 1
  • S. J. de Vries
    • 1
  1. 1.Bijvoet Center for Biomolecular Research, Faculty of ScienceUtrecht UniversityCH UtrechtThe Netherlands