Assessing the Precision and Recall of msTALI as Applied to an Active-Site Study on Fold Families

Abstract: Proteins execute various activities required by biological cells. Further, they structurally support and pro-mote important biochemical reactions which functionally are sparked by active-sites. Active-sites are regions where reac-tions and binding events take place directly; they foster pro-tein purpose. Describing functional relationships depends on factors that incorporate sequence, structure, and the biochem-ical properties of amino acids that form proteins. Our ap-proach to active-site description is computational, and many other approaches utilizing available protein data fall short of ideal. Successful recognition of functional interactions is cru-cial to advancements in protein annotation and the bioinfor-matics field at large. This research outlines our Multiple Structure Torsion Angle Alignment (msTALI) as a suitable strategy for addressing active-site identification by comparing results to other existing methods. Specifically, we address the precision of msTALI across three protein families. Our target proteins are PDBIDs 1A2B, 1B4V, 1B8S, 1COY, 1CXZ, 3COX, 1D7E, 1DPF, 1F9I, 1FTN, 1IJH, 1KOU, 1NWZ, 2PHY, and 1SIC.