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
de Vries S, Bonvin AMJJ (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Pept Prot Res 9:394–406
Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737
Karaca E, Bonvin AMJJ (2013) On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys. Acta Cryst D D69:683–694
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 9:1784–1794
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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 428:720–725
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© 2018 European Biophysical Societies' Association (EBSA)
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Bonvin, A.M.J.J. et al. (2018). HADDOCK. In: Roberts, G., Watts, A. (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35943-9_330-1
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DOI: https://doi.org/10.1007/978-3-642-35943-9_330-1
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