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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