Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking

A major problem in genome annotation is whether it is valid to transfer the function from a characterised protein to a homologue of unknown activity. Here, we show that one can employ a strategy that uses a structure-based pr ediction of protein functional sites to assess the reliability of functiona l inheritance. We have automated and benchmarked a method based on the evol utionary trace approach. Using a multiple sequence alignment, we identified invariant polar residues, which were then mapped onto the protein structur e. Spatial clusters of these invariant residues formed the predicted functi onal site. For 68 of 86 proteins examined, the method yielded information a bout the observed functional site. This algorithm for functional site predi ction was then used to assess the validity of transferring the function bet ween homologues. This procedure was tested on 18 pairs of homologous protei ns with unrelated function and 70 pairs of proteins with related function, and was shown to be 94% accurate. This automated method could be linked to schemes for genome annotation. Finally, we examined the use of functional s ite prediction in protein-protein and protein-DNA docking. The use of predi cted functional sites was shown to filter putative docked complexes with a discrimination similar to that obtained by manually including biological in formation about active sites or DNA-binding residues. (C) 2001 Academic Pre ss.