Encyclopedia of Biophysics

Living Edition
| Editors: Gordon Roberts, Anthony Watts, European Biophysical Societies

HADDOCK

  • Alexandre M. J. J. Bonvin
  • C. Geng
  • M. van Dijk
  • E. Karaca
  • P. L. Kastritis
  • P. I. Koukos
  • Z. Kurkcuoglu
  • A. S. J. Melquiond
  • J. P. G. L. M. Rogridues
  • J. Schaarschmidt
  • C. Schmitz
  • J. Roel-Touris
  • M. E. Trellet
  • S. de Vries
  • A. Vangone
  • L. Xue
  • G. C. P. van Zundert
Living reference work entry
DOI: https://doi.org/10.1007/978-3-642-35943-9_330-1

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; Rodrigues and Bonvin 2014). 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 (see Fig. 1). When experimental data are unavailable or scarce,...
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References

  1. de Vries S, Bonvin AMJJ (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Pept Prot Res 9:394–406CrossRefGoogle Scholar
  2. Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737CrossRefPubMedGoogle Scholar
  3. Karaca E, Bonvin AMJJ (2013) On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys. Acta Cryst D D69:683–694CrossRefGoogle Scholar
  4. Karaca E, Melquiond ASJ, de Vries SJ, Kastritis PL, Bonvin AMJJ (2010) Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multi-body docking server. Mol Cell Proteomics 9:1784–1794CrossRefPubMedPubMedCentralGoogle Scholar
  5. Melquiond ASJ, Bonvin AMJJ (2010) Data-driven docking: using external information to spark the biomolecular rendez-vous. In: Zacharrias M (ed) Protein-protein complexes: analysis, modeling and drug design. Imperial College Press, London, pp 183–209Google Scholar
  6. Rodrigues JPGLM, Bonvin AMJJ (2014) Integrative computational modeling of protein interactions. FEBS J 281:1988–2003CrossRefPubMedGoogle Scholar
  7. van Zundert GCP, Melquiond ASJ, Bonvin AMJJ (2015) Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-EM data. Structure 23:949–996CrossRefPubMedGoogle Scholar
  8. van Zundert GCP, Rodrigues JPGLM, Trellet ME, Schmitz C, Kastritis PL, Karaca E, Melquiond SJ, van Dijk M, de Vries SJ, Bonvin AMJJ (2016) The HADDOCK2.2 webserver: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720–725CrossRefPubMedGoogle Scholar

Copyright information

© European Biophysical Societies' Association (EBSA) 2018

Authors and Affiliations

  • Alexandre M. J. J. Bonvin
    • 1
  • C. Geng
    • 1
  • M. van Dijk
    • 1
  • E. Karaca
    • 1
  • P. L. Kastritis
    • 1
  • P. I. Koukos
    • 1
  • Z. Kurkcuoglu
    • 1
  • A. S. J. Melquiond
    • 1
  • J. P. G. L. M. Rogridues
    • 1
  • J. Schaarschmidt
    • 1
  • C. Schmitz
    • 1
  • J. Roel-Touris
    • 1
  • M. E. Trellet
    • 1
  • S. de Vries
    • 1
  • A. Vangone
    • 1
  • L. Xue
    • 1
  • G. C. P. van Zundert
    • 1
  1. 1.Bijvoet Center for Biomolecular Research, Faculty of ScienceUtrecht UniversityUtrechtThe Netherlands

Section editors and affiliations

  • Mitsu Ikura

There are no affiliations available