Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.

Lars Malmström, Michael Riffle, Charlie E M Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau, David Baker

Research output: Contribution to journalArticle

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 14,934 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 3,338 putative domains and assigned SCOP superfamily annotations to 581 of them. We have also assigned structural annotations to 7,094 predicted domains based on fold recognition and homology modeling methods. The domain predictions and structural information are available in an online database at http://rd.plos.org/10.1371_journal.pbio.0050076_01.

Original languageEnglish (US)
JournalPLoS Biology
Volume5
Issue number4
DOIs
StatePublished - Apr 2007

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Gene Ontology
Fungal Proteins
Proteome
proteome
Yeast
Ontology
Genes
Yeasts
yeasts
prediction
Databases
Molecular Conformation
Saccharomyces
Bayes Theorem
genes
proteins
protein structure
Saccharomyces cerevisiae
Genome
genome

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. / Malmström, Lars; Riffle, Michael; Strauss, Charlie E M; Chivian, Dylan; Davis, Trisha N.; Bonneau, Richard; Baker, David.

In: PLoS Biology, Vol. 5, No. 4, 04.2007.

Research output: Contribution to journalArticle

Malmström, Lars ; Riffle, Michael ; Strauss, Charlie E M ; Chivian, Dylan ; Davis, Trisha N. ; Bonneau, Richard ; Baker, David. / Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. In: PLoS Biology. 2007 ; Vol. 5, No. 4.
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