Proteins. 2006 Dec 1;65(4):922-9.

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

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University of Washington, Seattle, Washington 98195, USA.

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.

PMID:: 17034045; [PubMed - indexed for MEDLINE]

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