Poster Presenter

ProBiS Algorithm for Detection of Structurally Conserved Protein Binding Sites
Janez Konc and Dusanka Janezic
Slovenia

Detection of recurrent three-dimensional patterns of locally conserved physicochemical properties on the surface of a protein can be used to detect binding sites in proteins that may lack sequence and global structural conservation.

An algorithm, ProBiS is described which detects structurally conserved sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures with sub-residue precision and detects structurally conserved sites located on the protein surface with sub-residue precision. Using an efficient maximum clique algorithm, the program identifies proteins which share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural conservation scores are calculated for query protein's surface residues, which are then expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein-protein, protein-small ligand, and protein-DNA binding sites.