title: APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
abstract: APID (Agile Protein Interactomes DataServer) is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes. This resource is a new, fully redesigned server that includes a comprehensive collection of protein interactomes for more than 400 organisms (25 of which include more than 500 interactions) produced by the integration of only experimentally validated protein-protein physical interactions. For each protein-protein interaction (PPI) the server includes currently reported information about its experimental validation to allow selection and filtering at different quality levels. As a whole, it provides easy access to the interactomes from specific species and includes a global uniform compendium of 90,379 distinct proteins and 678,441 singular interactions. APID integrates and unifies PPIs from major primary databases of molecular interactions, from other specific repositories and also from experimentally resolved 3D structures of protein complexes where more than two proteins were identified. For this purpose, a collection of 8,388 structures were analyzed to identify specific PPIs. APID also includes a new graph tool (based on Cytoscape.js) for visualization and interactive analyses of PPI networks. The server does not require registration and it is freely available for use at http://apid.dep.usal.es.
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Alonso-López
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Gutiérrez
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain.
authors.forename: Katia P
authors.initials: KP
authors.lastname: Lopes
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Prieto
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Santamaría
authors.affiliation: Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain jrivas@usal.es.
authors.forename: Javier
authors.initials: J
authors.lastname: De Las Rivas
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000592:standards*; D060066:Protein Interaction Maps; D020543:Proteome / Q000378:metabolism*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D020543:Proteome