Detection of protein catalytic residues at high precision using local network properties

Background: Identifying the active site of an enzyme is a crucial step in functional studies. While protein sequences and structures can be experimentally characterized, determining which residues build up an active site is not a straightforward process. In the present study a new method for the detection of protein active sites is introduced. This method uses local network descriptors derived from protein three-dimensional structures to determine whether a residue is part of an active site. It thus does not involve any sequence alignment or structure similarity to other proteins. A scoring function is elaborated over a set of more than 220 proteins having different structures and functions, in order to detect protein catalytic sites with a high precision, i.e. with a minimal rate of false positives. Results: The scoring function was based on the counts of first-neighbours on side-chain contacts, third-neighbours and residue type. Precision of the detection using this function was 28....

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Patrick Slama, Ioannis Filippis, Michael Lappe
• Keywords: Active Site, BMCBI 2008, Protein, Scoring Function