title: The Proteome Folding Project: proteome-scale prediction of structure and function.
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 three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated 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.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Drew
authors.forename: Patrick
authors.initials: P
authors.lastname: Winters
authors.forename: Glenn L
authors.initials: GL
authors.lastname: Butterfoss
authors.forename: Viktors
authors.initials: V
authors.lastname: Berstis
authors.forename: Keith
authors.initials: K
authors.lastname: Uplinger
authors.forename: Jonathan
authors.initials: J
authors.lastname: Armstrong
authors.forename: Michael
authors.initials: M
authors.lastname: Riffle
authors.forename: Erik
authors.initials: E
authors.lastname: Schweighofer
authors.forename: Bill
authors.initials: B
authors.lastname: Bovermann
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Trisha N
authors.initials: TN
authors.lastname: Davis
authors.forename: Dennis
authors.initials: D
authors.lastname: Shasha
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
mesh_terms: D000818:Animals; D002826:Chorismate Mutase / Q000737:chemistry; D034301:Deinococcus / Q000378:metabolism / Q000528:radiation effects; D029721:Drosophila Proteins / Q000737:chemistry; D016678:Genome; D005964:Glucosyltransferases / Q000737:chemistry; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D009687:Nuclear Proteins / Q000737:chemistry / Q000145:classification; D010966:Plasmodium vivax / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry*; D015800:Protozoan Proteins / Q000737:chemistry; D011786:Quality Control; D015203:Reproducibility of Results; D011503:Transglutaminases / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D029721:Drosophila Proteins; D009687:Nuclear Proteins; D020543:Proteome; D015800:Protozoan Proteins; D011503:Transglutaminases; D005964:Glucosyltransferases; C527374:Rumi protein, Drosophila; D002826:Chorismate Mutase