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Full Record: APID  
Short NameAPID
Full NameAgile Protein Interactomes DataServer
Last ObservedJuly 26th, 2017
DescriptionAPID (Agile Protein Interactomes DataServer) is a new full redesigned biological resource 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. At present, as a whole APID includes a comprehensive compendium of more than 90,000 distinct proteins and more than 700,000 singular interactions. The analytical and integrative effort done in APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT), from other original resources (like BioPlex) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. In this way, more than 8,000 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). It also complies with PSI-MI standards.
Sample Data URL 
Data SourceSecondary
AvailabilityFree to all users
PubMed ArticlesAPID: Agile Protein Interaction DataAnalyzer.
Prieto C. and De Las Rivas J.
Nucl. Acids Res. 34: W298-W302.

APID2NET: unified interactome graphic analyzer.
Hernandez-Toro J, Prieto C, De las Rivas J.
Bioinformatics. 2007 Sep 15;23(18):2495-7.

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
Alonso-Lopez D, Gutierrez MA, Lopes KP, Prieto C, Santamaria R, De Las Rivas J.
Nucleic Acids Res. 2016 Jul 8;44(W1):W529-35.

Types of DataProtein-Protein Interactions
Types of Tools
Genes / Proteins: 94,587
Interactions / Reactions: 767,742
Last Content Update: June 1st, 2017
Major OrganismsArabidopsis thaliana, Escherichia coli, Bos taurus, Rattus norvegicus, Caenorhabditis elegans, Homo sapiens, Saccharomyces cerevisiae, Mus musculus, Schizosaccharomyces pombe, Danio rerio, Mycoplasma pneumoniae, Xenopus laevis, Drosophila melanogaster, Plasmodium falciparum, Helicobacter pylori, Bacillus subtilis
Relative Popularity23
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"Pathguide: the pathway resource list" is maintained by Gary Bader1.
The website was originally created by Michael Cary 2 and was significantly updated and redesigned by Vuk Pavlovic1.
Thanks to Emek Demir for the Pathguide name.

1. Bader Lab
2. Sander Group

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