The Skaggs School of Pharmacy & Pharmaceutical Sciences

Philip E. Bourne

Dr. Philip E. Bourne, Ph.D. is a Professor in the Skaggs School of Pharmacy and Pharmaceutical Sciences (SSPPS) and the Department of Pharmacology at the University of California San Diego (UCSD), Adjunct Professor at the Burnham Institute, and Associate Director of the Protein Data Bank (PDB). Dr. Bourne is a Past President of the International Society for Computational Biology, an elected fellow of the American Medical Informatics Association and Founding Editor-in-Chief of the open access journal PLoS Computational Biology, and a long standing member of the National Science Foundation and National Institutes of Health panels responsible for reviewing proposals relating to biological infrastructure and bioinformatics. Dr. Bourne is a past member of the US National Committee for Crystallography, past chairman of the International Union of Crystallography Computing Commission IUCrCC and past chairman of the American Crystallography Association (ACA) Computing Committee. Recent awards include the 2009 Benjamin Franklin award, the Flinders University Convocation Medal for Outstanding Achievement 2004 and the Sun Microsystems Convergence Award 2002. He has published over 200 papers and 5 books, one of which sold over 150,000 copies. He has co-founded 4 companies: ViSoft Inc., Protein Vision Inc., a company distributing independent films for free and most recently SciVee Inc. Dr. Bourne teaches courses in Pharmacy Informatics, Structural Bioinformatics and Professional Development.

Key Words: Drug Discovery, the Protein Data Bank, Evolution, Cell Signaling, Immunology, Scholarly Communication

Research Interests:

Our laboratory focuses on three fundamental questions. (1) What happens when you take a drug? Recent research has focused on polypharmacology and finding off-target binding sites for major pharmaceuticals and new chemical entities to better understand possible side effects and opportunities for repositioning these compounds. At the heart of our work are new and efficient algorithms for ligand binding site searching, which have established the possible cause of side effects of a class of drugs known as Select Estrogen Receptor Modulators (SERMs) that includes tamoxifen as well as a possible repositioning of COMT inhibitors to treat extreme drug resistant tuberculosis. At this time we are systematically analyzing a number of major pharmaceuticals. (2) What is the ancestoral history of protein structure? Protein structure is more conserved than protein sequence over long evolutionary timescales and reveals evolutionary relationships not see from sequence alone. We have exploited this to define a tree of life based on protein structure information, established that life was influenced by shifts in trace metal geochemistry in the ocean and most recently suggested the existence of two new type of proteosome and described events associated with the emergence of alternative splicing. Inherent in all our work with proteins are the development of new methods to study protein motion, protein-protein interactions, and protein-protein global and local comparison. We use these methods to study cell signaling and immunology. We maintain the RCSB Protein Data Bank as part of collaboration with Rutgers University. (3) Can we improve the way science is disseminated and comprehended? Out laboratory is an advocate of open access publishing to maximize the distribution and impact of science and we develop resources using video and the full text of articles to enhance the learning experience for K12 as well as professional scientists.

Selected Publications

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne (2000) The Protein Data Bank. Nucleic Acid Research 28(1), 235.

Structural Bioinformatics (2002) Ed. P.E. Bourne and H. Weissig, Wiley and Associates, NY.

P.E. Bourne (2003) Free access to publicly funded databases is vital Nature 421, 786.

B. Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M. Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S. Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette (2005) The Immune Epitope Database and Analysis Resource: From Vision to Blueprint. PLoS Biology, 3(3) e9.

S. Yang, R.F. Doolittle and P.E. Bourne (2005) Phylogeny Determined through Protein Domain Content Proc. Nat. Acad. Sci. (USA) 102(2): 373.

E. Scheeff and P.E. Bourne (2005) Structural Evolution of the Protein Kinase-Like Superfamily PLoS Comp. Biol. 1(5): e49.

C.L. Dupont, S.Yang, B. Palenik and P.E. Bourne (2006) Putative Imprints in Modern Proteomes of Ancient Shifts in Trace Metal Geochemistry Proc. Nat. Acad. Sci. (USA), 103(47) 17822.

J.L. Fink and P.E. Bourne (2007) Reinventing Scholarly Communication for the Electronic Age. CT Watch, 3(3) 26-31.

J. Ponomarenko and P.E. Bourne (2007) Antibody-Protein Interactions: Benchmark Datasets and Prediction Tools Evaluation BMC Structural Biology 7(1):64.

L. Xie, J. Wang and P.E. Bourne (2007) In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators. PLoS Comp. Biol., 3(11) e217.

R. Valas and P.E. Bourne (2008) Rethinking Proteasome Evolution: Two Novel Bacterial Proteasomes J. Mol. Evol., In Press.

J.L.Fink, S. Kushch, P. Williams & P.E.Bourne 2008 BioLit: Integrating Biological Literature with Databases NAR 36(S2) W385-389

L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments Proc. Nat. Acad. Sci. (USA), 105(14) 5441-5446.

S. Veretnik, C. Wills, P. Youkharibache, R. Valas & P.E. Bourne 2009 Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome, PLoS Comp. Biol.5(3) e10000315

Structural Bioinformatics 2nd Edition 2009 J. Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ.

L. Xie, J. Li, L. Xie, and P.E.Bourne 2009 Combinatorial Control of Interconnected Networks Plays a Key Role in the Modulation of Adverse Drug Reaction of Cholesterylester Transfer Protein Inhibitors, PLoS COmp. Biol. In Press.

S.L Kinnings, N. Buchmeier, N. Liu, P.J. Tonge L. Xie and P.E. Bourne 2009 Discovery of Novel Drug Leads to Treat Multi-drug and Extensively Drug Resistant Tuberculosis by Repositioning Safe Pharmaceuticals: A Chemical Genomics Approach with Subsequent Biological Validation. PLoS Comp. Biol. In Press.

List of Publications in Pub Med