title: JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.
abstract: The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2at large-scale on more than 20 000 chains. JET2strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET2on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein-protein interactions modulation and interaction surface redesign.
authors.affiliation: Sorbonne Universités, UPMC University Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France.
authors.forename: Hugues
authors.initials: H
authors.lastname: Ripoche
authors.affiliation: Sorbonne Universités, UPMC University Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Laine
authors.affiliation: CNRS UMR 5086/University Lyon I, Institut de Biologie et Chimie des Proteines, 69367 Lyon, France.
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Ceres
authors.affiliation: Sorbonne Universités, UPMC University Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France alessandra.carbone@lip6.fr.|Institut Universitaire de France, 75005 Paris, France.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Carbone
mesh_terms: D000818:Animals; D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D012984:Software