+ Present Address:
SmithKline Beecham Pharmaceuticals
Research & Development
Bioinformatics
New Frontiers Science Park
Harlow, Essex, CM19 5AW, U.K.

* To whom correspondence should be addressed.

A method is presented to assess the significance of binding site similarities within superimposed protein three-dimensional structures and applied to all similar structures in the protein databank. For similarities between three-dimensional structures lacking significant sequence similarity, the important distinction was made between remote homology (an ancient common ancestor) and analogy (likely convergence to a folding motif) according to the structural classification of proteins (SCOP) database. Supersites were defined as structural locations on groups of analogous proteins (ie. superfolds) showing a statistically significant tendancy to bind substrates despite little evidence of a common ancestor. The study identified three potentially new superfolds containing supersites: ferredoxin-like folds, four-helical bundles and double-stranded beta helices. In addition, the method quantified binding site similarities within homologous proteins and previously identified supersites such as that found in the beta-alpha (TIM) barrels. Implications for protein evolution, and the prediction of protein function either through fold recognition or tertiary structure comparison, are discussed.