title: Rosetta in CAPRI rounds 13-19.
abstract: Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13-19 we tested the ability of various backbone remodeling strategies to capture the main-chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large-scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Sarel J
authors.initials: SJ
authors.lastname: Fleishman
authors.forename: Jacob E
authors.initials: JE
authors.lastname: Corn
authors.forename: Eva M
authors.initials: EM
authors.lastname: Strauch
authors.forename: Tim A
authors.initials: TA
authors.lastname: Whitehead
authors.forename: Ingemar
authors.initials: I
authors.lastname: Andre
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.forename: James J
authors.initials: JJ
authors.lastname: Havranek
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Philip
authors.initials: P
authors.lastname: Bradley
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA