Structural analysis of protein complexes made easy

Most important molecular processes in the cell rely on the interaction between biomolecules. Therefore, the availability of a 3D structure of a biological complex and the characterization of the interacting interface is a fundamental step for possible biomedical and biotechnological applications. Unfortunately, the 3D structure of a significant fraction of biomolecular complexes is difficult to solve experimentally. In this scenario, protein-protein docking software is making this kind of simulations an effective tool to predict the 3D structure and the surface of interaction between the partners in biological complexes. However, correctly scoring the obtained solutions to extract native-like ones is still an open problem, highlighting the need for tools specifically developed to analysis the interface in biological complexes. For these reasons, we developed COCOMAPS,1 a web tool to analyse and visualize the interface in biomolecular complexes. COCOMAPS combines the traditional analysis and 3D visualization of biological complexes with the effectiveness of the contact map view. It can be applied to the analysis of both experimental and predicted 3D structures of biological complexes. Further, we used contact maps as the basis for novel tools, CONS-COCOMAPS,2 CONSRANK3,4 and MDcons,5 developed for the analysis of conformational ensembles of protein complexes, such as docking models and MD snapshots. Details on the above tools and results of their application to selected test-cases will be presented.