Distributions of beta sheets in proteins with application to structure prediction

TitleDistributions of beta sheets in proteins with application to structure prediction
Publication TypeJournal Article
Year of Publication2002
AuthorsRuczinski, I., Kooperberg C., Bonneau R., & Baker D.
JournalProteins
Volume48
Issue1
Pagination85-97
Date Published2002 Jul 1
ISSN1097-0134
KeywordsAlgorithms, Animals, Models, Molecular, Primary Publication, Probability, Protein Folding, Protein Structure, Secondary, Proteins, Sequence Analysis, Protein
Abstract

We recently developed the Rosetta algorithm for ab initio protein structure prediction, which generates protein structures from fragment libraries using simulated annealing. The scoring function in this algorithm favors the assembly of strands into sheets. However, it does not discriminate between different sheet motifs. After generating many structures using Rosetta, we found that the folding algorithm predominantly generates very local structures. We surveyed the distribution of beta-sheet motifs with two edge strands (open sheets) in a large set of non-homologous proteins. We investigated how much of that distribution can be accounted for by rules previously published in the literature, and developed a filter and a scoring method that enables us to improve protein structure prediction for beta-sheet proteins. Proteins 2002;48:85-97.

Alternate JournalProteins
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