APID (Agile Protein Interactomes DataServer) is a new full redesigned version of APID (previous resource published in Nucleic Acids Research 2006, 34 Web Server issue: W298-W302) that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. In this way, APID provides interactomes from specific organisms that in 25 cases have more than 500 proteins. As a whole APID includes a comprehensive compendium of 90,379 distinct proteins and 678,441 singular interactions.
The analytical and integrative effort done in APID unifies PPIs from primary databases of molecular interactions (BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. In this way, 8,388 structures have been analyzed to find specific protein-protein interactions reported with details of their molecular interfaces. APID also includes a new data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions (i.e. the reliability of the "edges" in the network) and an interactive mapping of the functional environment of the proteins (i.e. the functional annotations of the "nodes" in the network).
When using APID data, we would like you to provide REFERENCE to our work quoting the following publication: Alonso-López D, Gutiérrez MA, Lopes KP, Prieto C, Santamaria R, De Las Rivas J. APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Research 2016; doi: 10.1093/nar/gkw363.