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Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology.

Type Information
Nr 15 (Research article)
Authors Malmström, Lars; Riffle, Michael; Strauss, Charlie; Chivian, Dylan; Davis, Trisha; Bonneau, Richard; Baker, David
Title Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology.
Journal PLoS Biol (2007) 5 e76
DOI 10.1371/journal.pbio.0050076
Citations 61 citations (journal impact: 12.68)
Abstract Saccharomyces cerevisiae is one of the best-studied model organisms yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14934 domains and those lacking sequence similarity to proteins of known structure were folded using the Rosetta de novo structure prediction method on the World Community Grid. This structural data was integrated with process component and function annotations from the Saccharomyces Genome Database to assign yeast protein domains to SCOP superfamilies using a simple Bayesian approach. We have predicted the structure of 3338 putative domains and assigned SCOP superfamily annotations to 581 of them. We have also assigned structural annotations to 7094 predicted domains based on fold recognition and homology modeling methods. The domain predictions and structural information are available in an online database at httprd.plos.org10.1371_journal.pbio.0050076_01.