title: Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.
abstract: Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc.
authors: Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Hasup
authors: H
authors: Lee
authors: Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Minkyung
authors: M
authors: Baek
authors: Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Gyu Rie
authors: GR
authors: Lee
authors: Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Sangwoo
authors: S
authors: Park
authors: Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Chaok
authors: C
authors: Seok
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins
keywords: CAPRI; model refinement; protein loop modeling; protein oligomer structure