Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 78, Issue 15, Pages 3212-3218Publisher
WILEY
DOI: 10.1002/prot.22784
Keywords
CAPRI; structure prediction; protein-protein interactions; RNA-protein interactions; Rosetta; flexible-backbone modeling; conformational changes; docking; backrub; fragment insertion
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Funding
- NIH
- Human Frontier Science Program
- Jane Coffin Childs Fellowships
- Scientific Interface
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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. Proteins 2010; 78:3212-3218. (C) 2010 Wiley-Liss, Inc.
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