title: InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.
abstract: The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Jinchao
authors.initials: J
authors.lastname: Yu
authors.affiliation: INSERM UMR-S 973 Molécules Thérapeutiques in Silico, INSERM UMR-S 973, RPBS, Université Paris Diderot, 35 rue H. Brion, case 7113, Sorbone Paris Cité, 75205 Paris cedex 13, France.
authors.forename: Marek
authors.initials: M
authors.lastname: Vavrusa
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Jessica
authors.initials: J
authors.lastname: Andreani
authors.affiliation: INSERM UMR-S 973 Molécules Thérapeutiques in Silico, INSERM UMR-S 973, RPBS, Université Paris Diderot, 35 rue H. Brion, case 7113, Sorbone Paris Cité, 75205 Paris cedex 13, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Rey
authors.affiliation: INSERM UMR-S 973 Molécules Thérapeutiques in Silico, INSERM UMR-S 973, RPBS, Université Paris Diderot, 35 rue H. Brion, case 7113, Sorbone Paris Cité, 75205 Paris cedex 13, France pierre.tuffery@univ-paris-diderot.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Tufféry
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France guerois@cea.fr.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Guerois
mesh_terms: D019985:Benchmarking; D019143:Evolution, Molecular; D020407:Internet; D062105:Molecular Docking Simulation; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins