A computational approach for detecting peptidases and their specific inhibitors at the genome level

Background: Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2–5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms when it is not strictly controlled by specific inhibitors. In genome annotation a basic question is to predict gene function. Here we describe a computational approach that can filter peptidases and their inhibitors out of a given proteome. Furthermore and as an added value to MEROPS, a specific database for peptidases already available in the public domain, our method can predict whether a pair of peptidase/inhibitor can interact, eventually listing all possible predicted ligands (peptidases and/or inhibitors). Results: We show that by adopting a decision-tree approach the accuracy of PROSITE and HMMER in detecting separately the four major peptidase types (...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G. Mita, Rita Casadio
• Keywords: Basic Peptidase Function, BMCBI 2007, Decision-tree Approach, Fundamental Cellular Activities