INTREPID— INformation-theoretic TREe traversal for Protein functional site IDentification

Motivation: Identification of functionally important residues in prote-ins plays a significant role in biological discovery. Here we present INTREPID – an information-theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments. INTREPID uses a traversal of the phylo-geny in combination with a positional conservation score, based on Jensen-Shannon divergence, to rank positions in a multiple sequence alignment. While knowledge of protein 3D structure can significantly improve the accuracy of functional site identification, since structu-ral information is not available for a majority of proteins, INTREPID relies solely on sequence information. We evaluated INTREPID on two tasks: predicting catalytic residues and predicting specificity determinants. Results: In catalytic residue prediction, INTREPID provides signifi-cant improvements over Evolutionary Trace, ConSurf as well as over a baseline global conservation method on a a set of 100 manually curated enzymes from the Catalytic Site Atlas. In particular, INTRE-PID is able to better predict catalytic positions that are not globally conserved and hence, attains improved sensitivity at high values of specificity. We also investigated the performance of INTREPID as a function of the evolutionary divergence of the protein family. We found that INTREPID is better able to exploit the diversity in such families and that accuracy improves when homologs with very low sequence identity are included in an alignment. In specificity determinant prediction, when subtype information is known, INTREPID-SPEC, a variant of INTREPID, attains accuracies that are competitive with other approaches for this task. Availability: INTREPID is available for 16919 families in the PhyloFacts resourc