RT Journal
A1 Drew, Kevin
A1 Winters, Patrick
A1 Butterfoss, Glenn L.
A1 Berstis, Viktors
A1 Uplinger, Keith
A1 Armstrong, Jonathan
A1 Riffle, Michael
A1 Schweighofer, Erik
A1 Bovermann, Bill
A1 Goodlett, David R.
A1 Davis, Trisha N.
A1 Shasha, Dennis
A1 Malmström, Lars
A1 Bonneau, Richard
T1 The Proteome Folding Project: Proteome-scale prediction of structure and function
JF Genome Research 
JO Genome Research 
YR 2011 
FD November 01 
VO 21 
IS 11 
SP 1981 
OP 1994 
DO 10.1101/gr.121475.111 
UL http://genome.cshlp.org/content/21/11/1981.abstract 
AB 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.