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 by...
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References
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.
de Vries SJ, van Dijk M, Bonvin AMJJ. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010;5:883–97.
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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.
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.91
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Bonvin, A.M.J.J. et al. (2013). HADDOCK. In: Roberts, G.C.K. (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16712-6_330
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DOI: https://doi.org/10.1007/978-3-642-16712-6_330
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