title: Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI.
abstract: The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed. Proteins 2017; 85:391-398. © 2016 Wiley Periodicals, Inc.
authors: Physics Department T38, Technische Universität München, Garching, 85748, Germany.|Center for Integrated Protein Science Munich, München, 81377, Germany.
authors: Christina E M
authors: CE
authors: Schindler
authors: Physics Department T38, Technische Universität München, Garching, 85748, Germany.
authors: Isaure
authors: I
authors: Chauvot de Beauchêne
authors: Physics Department T38, Technische Universität München, Garching, 85748, Germany.
authors: Sjoerd J
authors: SJ
authors: de Vries
authors: Physics Department T38, Technische Universität München, Garching, 85748, Germany.|Center for Integrated Protein Science Munich, München, 81377, Germany.
authors: Martin
authors: M
authors: Zacharias
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D062105:Molecular Docking Simulation / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods* / Q000706:statistics & numerical data; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D010455:Peptides; D011506:Proteins
keywords: docking minimization; elastic network model; induced fit; protein-protein complex formation; protein-protein interaction