All residues in a protein are not equally important. Some are essential to maintain the proper structure and function of the protein, while others tolerate replacement by different amino acids. Identifying the functionally important sites in a protein is an important step towards characterizing its molecular function. In this talk, I will describe a recent fast algorithm for predicting functionally important sites using evolutionary conservation. I will then introduce a method that combines this conservation measure with information from 3D structures to significantly improve the state-of-the-art in identifying ligand-binding sites.

Capra JA and Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics, 23(15):1875-82, 2007.

Capra JA and Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics, 24(13) 1473-1480, 2008.

Capra JA, Singh M, and Funkhouser T. Combining Evolutionary Conservation and 3D Structure to Predict Ligand Binding Sites. In preparation.