Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation

TitleImproved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
Publication TypeJournal Article
Year of Publication2006
AuthorsBradley, P., & Baker D.
JournalProteins
Volume65
Issue4
Pagination922-9
Date Published2006 Dec 1
ISSN1097-0134
KeywordsAnimals, Computer Simulation, Databases, Protein, Humans, Models, Molecular, Primary Publication, Protein Folding, Protein Structure, Secondary, Proteins
Abstract

Proteins with complex, nonlocal beta-sheets are challenging for de novo structure prediction, due in part to the difficulty of efficiently sampling long-range strand pairings. We present a new, multilevel approach to beta-sheet structure prediction that circumvents this difficulty by reformulating structure generation in terms of a folding tree. Nonlocal connections in this tree allow us to explicitly sample alternative beta-strand pairings while simultaneously exploring local conformational space using backbone torsion-space moves. An iterative, energy-biased resampling strategy is used to explore the space of beta-strand pairings; we expect that such a strategy will be generally useful for searching large conformational spaces with a high degree of combinatorial complexity.

Alternate JournalProteins
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