title: Information-driven structural modelling of protein-protein interactions.
abstract: Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes.
authors.affiliation: Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
authors.forename: João P G L M
authors.initials: JP
authors.lastname: Rodrigues
authors.forename: Ezgi
authors.initials: E
authors.lastname: Karaca
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D019295:Computational Biology; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software; D013816:Thermodynamics
chemical_list: D029968:Escherichia coli Proteins