title: Flexible docking and refinement with a coarse-grained protein model using ATTRACT.
abstract: A coarse-grained (CG) protein model implemented in the ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI Rounds 22-27. For six targets, acceptable or better quality solutions have been submitted corresponding to ~60% of all targets. For one target, promising results on the prediction of the hydration structure at the protein-protein interface have been achieved. New approaches for the rapid flexible refinement have been developed based on a combination of atomistic representation of the bonded geometry and a CG description of nonbonded interactions. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
authors.affiliation: Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.
authors.forename: Sjoerd
authors.initials: S
authors.lastname: de Vries
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D018360:Crystallography, X-Ray; D023281:Genomics; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
keywords: docking minimization; elastic network model; induced fit; protein-protein complex formation; protein-protein interaction