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The theme of this presentation is to describe computational studies that use information about protein structure to provide enhanced interpretation of biological data. First, a database that describes structural and functional annotation of the proteins in recently sequenced genomes w ill be reported (1). 40% of the human proteome can be assigned to domains of known structure. Comparative analysis of domain frequencies between different species provides insight into protein evolution. Second, the application of protein structure prediction by fold recognition will be reported (2). Despite the advances of sequence-based methods, fold recognition can identify additional probable remote homologies with its consequential suggestion of protein structure and function. The added value of expert intervention into contemporary algorithms will be assessed. Finally, recent studies to understand the evolution of metabolic networks using structural information to identify remote homologies will be reported (3). Programs available for use by the community are available at www.sbg.bio.ic.ac.uk. References: (1) Alves, R., Chaeleil, R. A. G. & Sternberg, M. J. E. (2002). Evolution of enzymes in metabolism: a network perspective. J. Mol. Biol. in the press. (2) Bates, P. A., Kelley, L. A., MacCallum, R M. & Sternberg, M. J. E. (2001). Enhancement of protein modelling by human intervention in applying the automatic prgrams 3D-JIGSAW and 3D-PSSM. Proteins Supplement 5, 39-46. (3) Muller, A, MacCallum, R.M. & Sternberg, M.J.E. (2002) A comparative analysis of proteins from the Human Genome. Genome Research in the press.

Exploiting protein structure in the post genome era