Distributions of beta sheets in proteins with application to structure prediction

Ingo Ruczinski, Charles Kooperberg, Richard Bonneau, David Baker

Research output: Contribution to journalArticle

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 β-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 β-sheet proteins.

Original languageEnglish (US)
Pages (from-to)85-97
Number of pages13
JournalProteins: Structure, Function and Genetics
Volume48
Issue number1
DOIs
StatePublished - Jul 1 2002

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Proteins
Simulated annealing
Research Design
beta-Strand Protein Conformation

Keywords

  • Beta sheets
  • Protein folding
  • Rosetta
  • Structure prediction

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Distributions of beta sheets in proteins with application to structure prediction. / Ruczinski, Ingo; Kooperberg, Charles; Bonneau, Richard; Baker, David.

In: Proteins: Structure, Function and Genetics, Vol. 48, No. 1, 01.07.2002, p. 85-97.

Research output: Contribution to journalArticle

Ruczinski, Ingo ; Kooperberg, Charles ; Bonneau, Richard ; Baker, David. / Distributions of beta sheets in proteins with application to structure prediction. In: Proteins: Structure, Function and Genetics. 2002 ; Vol. 48, No. 1. pp. 85-97.
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