title: GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.
abstract: Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure database or by ab initio docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion.
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Minkyung
authors.initials: M
authors.lastname: Baek
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Taeyong
authors.initials: T
authors.lastname: Park
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Lim
authors.initials: L
authors.lastname: Heo
authors.affiliation: Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Chiwook
authors.initials: C
authors.lastname: Park
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Chaok
authors.initials: C
authors.lastname: Seok
mesh_terms: D000595:Amino Acid Sequence; D019985:Benchmarking; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins