This is the era of biology, and at this moment in time, structural biology as manifest in the various structural genomics project under way worldwide. With protein structures at center stage comes the need for further structure characterization, more informed decisions about which new structures to determine, and the need for new tools to associate structure with function. This group, who through the PI, are already entrusted with the query and distribution of all structure data as deposited with the Protein Data Bank (PDB), propose a new community service to enable the science of structure genomics. The service will provide and new algorithms, associated software tools, and data (collectively referred to as the resource) to facilitate the process of high throughput structure determination and the interpretation of that large body of new structure data in a semi-automated process. Specifically the resource will: (i) facilitate structure genomics by guiding target selection towards new folds and/or biological function; (ii) provide functional annotation to newly determine structures of unknown function; and (iii) provide a comprehensive database of comparative (homology) models. The proposal brings together researchers from the University of California San Diego (UCSD), The Burnham Institute (TBI) and The Keck Graduate Institute (KGI) who will provide a public Web-accessible computing resource with associated software and data for use by all of the structural genomics community. The resource will be located at the San Diego Supercomputer Center (SDSC) which has a record of delivery high quality services to the biology community. The proposed public resource will complement the private software and data resulting from the individual structural genomics centers as they undertake competitive high throughput structure determination.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BBCB (01))
Program Officer
Edmonds, Charles G
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Biostatistics & Other Math Sci
Schools of Arts and Sciences
La Jolla
United States
Zip Code
Porta-Pardo, Eduard; Godzik, Adam (2016) Mutation Drivers of Immunological Responses to Cancer. Cancer Immunol Res 4:789-98
Xie, Li; Ng, Clara; Ali, Thahmina et al. (2013) Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics 14 Suppl 3:S9
Stegle, Oliver; Denby, Katherine J; Cooke, Emma J et al. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. J Comput Biol 17:355-67
Valas, Ruben E; Yang, Song; Bourne, Philip E (2009) Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol 19:329-34
Podtelezhnikov, Alexei A; Wild, David L (2009) Reconstruction and stability of secondary structure elements in the context of protein structure prediction. Biophys J 96:4399-408
Veretnik, Stella; Wills, Christopher; Youkharibache, Philippe et al. (2009) Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol 5:e1000315
Briedis, Kristine M; Starr, Ayelet; Bourne, Philip E (2008) Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PLoS One 3:e1597
Borgwardt, Karsten (2008) Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. Bioessays 30:707-10
Xie, Lei; Bourne, Philip E (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105:5441-6
Chung, Jo-Lan; Wang, Wei; Bourne, Philip E (2007) High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics 8:223

Showing the most recent 10 out of 55 publications