FAST ESTIMATION OF SURFACE COMPLEMENTARITY IN PROTEIN COMPLEXES

Giacomo Franzot^a and Oliviero Carugo^b

^a International School for Advanced Studies, via Beirut 4, 34014 Trieste, Italy and Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park 34012 Basovizza, Trieste, Italy

^b Department of General Chemistry, Pavia University, viale Taramelli 12, 27100 Pavia, Italy and
TASC-INFM National Laboratory, Strada Statale 14 - km 163,5 in AREA Science Park 34012 Basovizza, Trieste, Italy

Abstract

A novel measure of protein surface complementarity, sc_pride, is proposed. Each surface patch is represented by the distribution of the inter-atomic distances and the degree of similarity between two surface patches is estimated via a contingency table analysis of their two inter-atomic distance distributions. Such a low resolution surface representation allows very fast complementarity estimations that could find applications in protein-protein interaction prediction. The performance of sc_pride is compared to that of other surface complementarity measures with a very large set of protein-protein complexes obtained with docking simulations and the ability of sc_pride to recognize the surface complementarity is tested on a non-redundant set of experimentally determined crystal structures of protein-protein complexes.

Key words: protein structure, protein-protein interaction, protein surface