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The proteome folding project: Proteome-scale prediction of structure and function.

Citation Drew, Kevin; Winters, Patrick; Butterfoss, Glenn; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David; Davis, Trisha; Shasha, Dennis; Malmstrom, Lars; Bonneau, Richard; The proteome folding project: Proteome-scale prediction of structure and function. Genome Res (2011), 21: 1981-94.
Abstract The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition and grid-computing enabled de novo structure prediction. We predict protein domain boundaries and 3D structures for protein domains from 94 genomes (including Human, Arabidopsis, Rice, Mouse, Fly, Yeast, E. coli and Worm). De novo structure predictions were distributed on a grid of over 1.5 million CPUs worldwide (World Community Grid). We generate significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions.
Synopsis This paper describes a computational workflow used to annotate genomes, both with structure and function. In short, all ORFs found in a genome are parsed into structural domains and tertiary models are subsequently created for each domain. The structures are use to predict molecular function for each domain.
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