Prediction of protein-protein interactions based on surface patch comparison.
A method to predict if two proteins interact, based on their three-dimensional structures, is presented. It consists of five steps: (i) the surface of each protein, represented by the solvent accessible atoms, is divided into small patches; (ii) the shape of each patch is described by the atom distributions along its principal axes; (iii) the shape complementarity between two patches is estimated by comparing, through contingency table analysis, their atom distributions along their principal axes; (iv) given protein A, with nA surface patches, and protein B, with nB surface patches, nA x nB shape complementarity values are obtained; and (v) the distribution of the latter allows one to discriminate pairs of interacting and of noninteracting proteins. Only a few seconds are necessary to predict if two proteins interact, with accuracy close to 80%, sensitivity over 70% and specificity close to 50%.
Carugo
Oliviero
O
Department of General Chemistry, Pavia University, Pavia, Italy. carugo@tasc.infm.it
Franzot
Giacomo
G
D019295:Computational Biology; D016208:Databases, Factual; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012680:Sensitivity and Specificity; D013499:Surface Properties
D011506:Proteins