Protein surface conservation in binding sites.
An algorithm is described which uses the conservation of the 3D structure of protein surfaces, as opposed to their sequences, to detect protein-protein binding sites. The protein in which protein-protein binding sites are sought is compared with structures of multiple structurally related proteins and the surface that is conserved at least once is considered to be a part of the binding site. The binding site predictions obtained in this way for a set of protein-protein complexes correspond well with the actual protein-protein binding sites. A comparison of this method with an algorithm using the support vector machine approach for predicting protein-protein binding sites shows structural conservation to be an important characteristic that distinguishes binding sites from the remainder of protein surfaces.
Carl
Nejc
N
National Institute of Chemistry, Ljubljana, Slovenia.
Konc
Janez
J
Janezic
Dusanka
D
D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D017124:Conserved Sequence; D008958:Models, Molecular; D010444:Peptide Elongation Factor Tu / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012680:Sensitivity and Specificity; D013499:Surface Properties; D035181:TATA-Box Binding Protein / Q000737:chemistry / Q000378:metabolism; D051981:Uracil-DNA Glycosidase / Q000737:chemistry / Q000378:metabolism
D011506:Proteins; D035181:TATA-Box Binding Protein; D051981:Uracil-DNA Glycosidase; D010444:Peptide Elongation Factor Tu