title: Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.
abstract: In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.
authors.affiliation: Department of Sciences and Technologies, University "Parthenope" of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy. romina.oliva@uniparthenope.it.
authors.forename: Romina
authors.initials: R
authors.lastname: Oliva
authors.affiliation: Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia. edrisse.chermak@kaust.edu.sa.
authors.forename: Edrisse
authors.initials: E
authors.lastname: Chermak
authors.affiliation: Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia. luigi.cavallo@kaust.edu.sa.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
mesh_terms: D015195:Drug Design; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: CAPRI; COCOMAPS; CONSRANK; analysis; consensus; contact maps; docking decoys; docking models; inter-molecular contacts; interface; protein-protein interactions; ranking; scoring; structure prediction