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

ABSTRACT:

Motivation

Identification of functionally important residues in proteins 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 (MSAs). INTREPID uses a traversal of the phylogeny in combination with a positional conservation score, based on Jensen-Shannon divergence, to rank positions in an MSA. While knowledge of protein 3D structure can significantly improve the accuracy of functional site identification, since structural 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

SUBMITTER: Sankararaman S 

PROVIDER: S-EPMC2572704 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature