Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

Richard Bonneau, Charlie E M Strauss, David Baker

Research output: Contribution to journalArticle

Abstract

This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume43
Issue number1
DOIs
StatePublished - Apr 1 2001

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Keywords

  • Ab initio structure prediction
  • Homology
  • Rosetta

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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