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

TitleImproving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
Publication TypeJournal Article
Year of Publication2001
AuthorsBonneau, R., Strauss C. E., & Baker D.
JournalProteins
Volume43
Issue1
Pagination1-11
Date Published2001 Apr 1
ISSN0887-3585
KeywordsAlgorithms, Amino Acid Motifs, Amino Acid Sequence, Molecular Sequence Data, Phylogeny, Primary Publication, Protein Conformation, Protein Folding, Protein Structure, Secondary, Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Software
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. Proteins 2001;43:1-11.

Alternate JournalProteins
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