Faculty

Professor of Pharmacology

Key Words: Biological Databases; Ontologies; Computational Methods; Cell Signalling; Apoptosis.

Our group focuses on bioinformatics and structural bioinformatics in particular. We are members of the Research Collaboratory for Structural Informatics (RCSB) and have responsibility for the worldwide distribution and query of the Protein Data Bank (PDB). The computational aspects of our research focus on ontologies, data models, query languages, tools for comparative structure analysis and classification and visualization techniques. Practically we make available to the biology community algorithms and databases associated with signal transduction and apoptosis. We are interested in training students in effective use of the large amounts of biological data being generated by the human genome project and structural genomics. Examples of specific projects are:

• The Protein Data Bank (PDB) http://www.pdb.org.
• The Encyclopedia of Life (EOL) http://eol.sdsc.edu.
• The Protein Kinase Resource (PKR) http://pkr.sdsc.edu.
• Algorithms for searching and characterizing protein fold space http://cl.sdsc.edu/ce.html.
• Characterization of proteins involved in apoptosis http://www.apoptosis-db.org.
• Visualization of biological data http://mbt.sdsc.edu.
• Study of the effects of post-translational modification on protein structure http://pmr.sdsc.edu.

Selected Publications

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

W.W. Li1, G.B. Quinn, N. N. Alexandrov, P.E. Bourne and I.N. Shindyalov (2003) Proteins of Arabidopsis thaliana (PAT) database: A resource for comparative proteomics Genome Biology 4(8), R51

K.S. Doctor, J. Reed, A. Godzik and P.E.Bourne (2003) The Apoptosis Database Cell Death and Differentiation 10(6), 621-633.

P.E. Bourne and H. Weissig (2002) Structural Bioinformatics Wiley and Sons Inc., NY.

J.V. Ponaramenko, I.N. Shindyalov and P.E. Bourne (2002) Building an Automated Classification of DNA-binding Protein Domains Bioinformatics 18:S192-201.

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne Nucleic Acid Research (2000) 28(1), 235-242. The Protein Data Bank.

I.N. Shindyalov and P.E. Bourne (2000) Proteins: Structure, Function and Genetics 38(3), 247-260. An Alternative View of Protein Fold Space.