Towards protein interaction analysis through surface labeling

Abstract

The knowledge of the biological function of proteins would have great impact on the identification of novel drug targets, and on finding the molecular causes of diseases. Unfortunately, the experimental determination of protein function is a very expensive and time consuming process. As a consequence, the development of computational techniques to complement and guide the experimental process is a crucial and fundamental step for biological analysis. The final goal of the activity here presented is to provide a method that allows the identification of sites of possible protein-protein and protein-ligand interaction on the basis of the geometrical and topological structure of protein surfaces. The goal is then to discover complementary regions (that is with concave and convex segments that match each others) among different proteins. In particular, we are considering the first step of this process: the segmentation of the protein surface in protuberances and inlets through the analysis of convexity and concavity. To this end, two approaches will be described with a comparative assessment in terms of accuracy and speed of execution. © 2009 Springer Berlin Heidelberg.