Last update:   January 5, 2011
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Databases & Data Collections
Experimental Data
Related Domain, Pathway and Network Databases
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Databases & Data Collections

Experimental Data

  • Alanine Scanning Energetics DataBase
  • database of hotspots in 3D protein structures (University of Toronto)
  • bacterial protein interaction database
  • database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase
BID Wiki
  • Binding Interface Database
  • organize vast amounts of protein interaction information into tabular form, graphical contact maps, and descriptive functional profiles
BioGRID (Samuel Lunenfeld Research Institute)
  • The General Repository for Interaction Datasets
  • database of genetic and physical interactions
BOND (Thomson Corp.)
  • Biomolecular Object Network Databank
  • new resource to perform cross-database searches of available sequence, interaction, complex and pathway information
  • integrates a range of component databases including Genbank and BIND, the Biomolecular Interaction Network Database
Campylobacter jejuni Interactions Database (Wayne State University)
  • includes protein interaction data from a large-scale yeast two-hybrid (YTH) screen and interactions predicted from experimental data in other organisms (interologs)
  • Database of Interacting Proteins
DroID (Wayne State University)
  • DROsophila Interactions Database
  • comprehensive gene and protein interactions database designed specifically for the model organism Drosophila
EchoBASE (University of York)
  • integrated post-genomic database for E. coli
GWIDD (University of Kansas)
  • Genome WIde Docking Database
  • combines available experimental data with models built by docking techniques
  • contains known protein-protein interactions and allows input of other sequences and structures to find interacting proteins and obtain the structure of their complexes
HCPIN - Human Cancer Pathway Protein Interaction Network (Rutgers University)
  • constructed by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions
HIV-1 - Human Protein Interaction Database (NCBI)
  • summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV / AIDS
hp-DPI (National Health Research Institutes)
  • Helicobacter Pylori Database of Protein Interactomes
  • combined with experimental and inferring interactions
HPID (Inha University)
  • Human Protein Intercation Database
HUGE ppi (Kazusa DNA Research Institute)
  • database of protein-protein interactions between large KIAAproteins
  • HUGE: Human Unidentified Gene-Encoded large proteins
Human Protein Reference Database (Johns Hopkins University & The Institute of Bioinformatics, India)
  • platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome
I2D (Ontario Cancer Institute)
  • Interologous Interaction Database
  • database of known and predicted mammalian and eukaryotic protein-protein interactions
  • Inferred Biomolecular Interactions Server
  • reports physical interactions observed in experimentally-determined structures for a given protein
  • infers/predicts interacting partners and binding sites by homology
ICBS (University of California)
  • Inter-Chain Beta-Sheets database
  • protein-protein interactions mediated by interchain -sheet formation
KDBI (National University of Singapore)
  • database of Kinetic Data of Bio-molecular Interactions
KEGG BRITE (Kyoto University)
  • Biomolecular Relations in Information Transmission and Expression
  • functional hierarchies and binary relationships of biological entities
MINT (CBM, Rome)
  • Molecular INTeractions database
  • database of functional interactions between biological molecules: RNA, DNA, proteins
    • DOMINO - domain peptide interactions database, describing interactions mediated by protein-interaction domains
    • VirusMint - Virus protein interactions database (Yale University)
  • database of macromolecular movements with associated tools for flexibility and geometric analysis
MPact (MIPS)
MPIDB (J. Craig Venter Institute)
  • Microbial Protein Interaction DataBase
  • provide all known physical microbial interactions
  • experimentally determined interactions among proteins of 250 bacterial species/strains
  • Mammalian Protein-Protein Interaction database
  • collection of manually curated high-quality PPI data collected from the scientific literature by expert curators
NetPro (Molecular Connections)
  • database of protein-protein and protein-small molecules interaction
  • consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references
PDZBase (Weill Medical College of Cornell University)
  • manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains
  • currently contains 339 experimentally determined protein-protein interactions
PepCyber: P~PEP (University of Minnesota)
  • database of human protein-protein interactions mediated by phosphoprotein binding domains (PPBDs)
  • Protein-protein INteraction Thermodynamic database
  • contains experimental data of several thermodynamic parameters along with literature, sequence and structural information and experimental conditions
POINT (National Health Research Institutes & National Taiwan University)
  • functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets
  • integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome
PRIME (Human Genome Center, University of Tokyo)
  • PRotein Interaction and Molecular Information databasE
  • integrated gene/protein informatics database based on natural language processing
ProtoArray® (Invitrogen)
Protein Interaction Maps - PIMs (Hybrigenics)
  • functional proteomics software platform, dedicated to the exploration of protein pathways
  • PIM's available for Helicobacter pylori, Hiv_Human, Drosophila and TGF-Beta
Protein-Protein Interaction Panel using mouse full-length cDNAs (RIKEN, Yokohama Institute)
  • see Suzuki et al., Genome Res. 2001, 11, 1758-1765. [PubMed]
PSIbase (BioSystems Dept., KAIST & BiO centre)
  • molecular interaction database
  • focuses on structural interaction of proteins and their domains
PutidaNET (Korean BioInformation Center)
  • proteome database of Pseudomonas putida KT2440
  • provides predicted protein-protein interaction, gene ontology information, and physio-chemical information
SNAPPIView (University of Dundee)
  • Structures, iNterfaces and Alignments for Protein-Protein Interactions
  • object-oriented database of domain-domain interactions observed in structural data
  • database of two-hybrid protein interactions in B. Subtilis
SPIN-PP Server (Columbia University)
  • Surface Properties of INterfaces - Protein Protein interfaces
  • database of all protein-protein interfaces in the PDB
Yeast Interacting Proteins Database (Kanazawa University)
Yeast Protein Linkage Map Data (University of Washington)
  • Yeast Proteome Database
  • comprehensive knowledge resource for the proteins of S. cerevisiae

Databases & Data Collections


  • prediction of protein-protein interAction of moDular domAiNs
Arabidopsis Interactions Viewer (CSB University of Toronto)
  • database of 70944 predicted and 4300 confirmed Arabidopsis interacting proteins
AtPID (Northeast Forest University)
  • Arabidopsis Thaliana Protein Interactome Database
  • centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome
  • integrates data from several bioinformatics prediction methods and manually collected information from the literature
cons-PPISP (Florida State University)
  • consensus protein-protein interaction site predictor
  • consensus neural network method for predicting protein-protein interaction sites
Fly-DPI ( National Health Research Institutes)
  • Drosophila melanogaster database of protein interactomes
  • statistical model to predict protein interaction networks
Genes2Networks (Mount Sinai School of Medicine)
  • connecting lists of gene symbols using mammalian protein interactions databases
  • powerful web-based software that can help to interpret lists of genes and proteins
  • can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes
HAPPI (Indiana University School of Informatics, Purdue University School of Science)
  • Human Annotated and Predicted Protein Interaction database
  • collected or inferred computationally from public sources
INTERPARE (National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology & BiO Centre)
  • protein interfaceome database
  • contains large-scale interface data of proteins with known 3D-structures
meta-PPISP (Florida State University)
  • meta web server for protein-protein interaction site prediction
MitoInteractome (Korean Bioinformation Center)
  • web-based portal containing information on predicted protein-protein interactions, physico-chemical properties, polymorphism, and diseases related to the mitochondrial proteome
  • contains 6,549 protein sequences which were extracted from the following databases: SwissProt, MitoP, MitoProteome, HPRD and Gene Ontology database
NOXclass (Max-Planck-Institut für Informatik)
  • SVM (support vector machine algorithm) classifier identifying protein-protein interaction types
PIBASE (University of California)
  • comprehensive database of structurally defined interfaces between pairs of protein domains
PIPs (University of Dundee)
  • human protein-protein interaction prediction
PPIDB (Iowa State University)
  • database of protein-protein interfaces derived from all protein-protein complexes available in the Protein Data Bank
Predictome (Boston University)
  • database of putative links between proteins using sequence data of genomes of 71 microorganisms
  • PRotein Interaction and MOlecule Search database
  • knowledge portal for analysing protein-protein interaction data
PRISM (Koc University)
  • PRotein Interactions by Structural Matching
  • explore protein interfaces and predict protein-protein interactions
  • web service to functionally classify genes/proteins from any type of interaction network
Prolinks Database (University of California)
  • collection of inference methods used to predict functional linkages between proteins
  • methods include the Phylogenetic Profile method, which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage
Protein Interaction Network of E. coli (Centre for DNA Fingerprinting and Diagnostics)
  • obtained by training a Support Vector Machine on the high quality of interactions in the EcoCyc database, and with the assumption that the periplasmic and cytoplasmic proteins may not interact with each other [PubMed]
SNAPPI-Predict (University of Dundee)
  • Structures, iNterfaces and Alignments for Protein-Protein Interactions
  • protein-protein interaction prediction program
SPIDer (Beijing Normal University)
  • Saccharomyces Protein-protein Interaction Database
  • effective method of reconstructing a yeast protein interaction network by measuring relative specificity similarity (RSS) between two Gene Ontology (GO) terms
SynechoNET (Korean BioInformation Center)
  • integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
  • shows feasible cyanobacterial domain-domain interactions, as well as their protein level interactions
  • provides transmembrane topology and domain information, as well as the interaction networks in graphical web interfaces

Databases & Data Collections

Related Domain, Pathway and Network Databases

BioCarta (BioCarta)
  • charting pathways of life
BioCyc Database Collection (SRI)
  • collection of 506 pathway/genome databases
  • each database describes the genome and metabolic pathways of a single organism
BN++ (Center for Bioinformatics Saar & Center for Bioinformatics Tübingen)
  • biochemical network library for analyzing and visualizing complex biochemical networks and processes
CellCircuits (University of California)
  • open-access database of molecular network models that bridges the gap between databases of individual pair-wise molecular interactions and databases of validated pathways
  • contains functional network hypothesis produced by algorithms that screen molecular interaction networks based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species
DAPID (National Chiao Tung University)
  • Domain Annotated Protein-protein Interaction Database
  • database of domain-annotated protein interactions inferred from three-dimensional (3D) interacting domains of protein complexes in the Protein Data Bank (PDB)
  • Domain Interaction MAp
  • comprehensive resource for functional and physical interactions among conserved protein-domains
DOMINE (University of Texas at Dallas)
  • database of known and predicted protein domain (domain-domain) interactions
  • Database Of Quantitative Cellular Signaling
EDGEdb (University of Massachusetts Medical School)
  • C. Elegans Differential Gene Expression database
EMP (EMP Project Inc.)
  • Enzymes and Metabolic Pathways
HotSprint (KOC University, Turkey)
  • database of computational hot spots in protein interfaces
iHOP (Computational Biology Center, Memorial Sloan-Kettering Cancer Center, USA & Protein Design Group, National Center of Biotechnology, Spain)
  • Information Hyperlinked Over Proteins
  • gene network for navigating the literature
InterDom (Laboratories for Information Technology)
  • database of putative INTERacting protein DOMains derived from multiple sources
  • database of chemical compounds and reactions in biological pathways
Kinase Pathway Database (Human Genome Center)
  • integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface
Negatome Database (MIPS)
  • collection of protein and domain pairs which are unlikely engaged in direct physical interactions
  • contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analysing protein complexes from the PDB
  • can be used to evaluate newly derived experimental interactions
PATHWAY Database (ProteinLounge)
  • largest collection of signal transduction and metabolic pathways including extensive reviews and detailed protein information
Pfam (Sanger Institute)
  • Protein FAMilies database of alignments and HMM
PPISearch (National Chiao Tung University)
  • web server for searching homologous protein-protein interactions across multiple species
SCOPPI (TU Dresden)
  • Structural Classification Of Protein-Protein Interfaces
  • database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions
  • Structural Characterization Of Water, Ligands and Proteins
  • web application represent a framework for the study of protein interfaces and comparative analysis of protein family binding regions
SMART (EMBL Heidelberg)
  • Simple Modular Architecture Research Tool
SPAD (Kyushu University)
  • Signaling PAthway Database
  • integrated database for genetic information and signal transduction systems
  • database of composite regulatory elements affecting gene transciption in eukaryotes [Guided Tour]
  • database on molecular pathways and cellular network modelling [Guided Tour]
UniHI (Charite - Medical Devision, Humboldt-University zu Berlin)
  • Unified Human Interactome
  • comprehensive database of the computational and experimental based human protein interaction networks
The Interactive Fly (Society for Developmental Biology)
  • a guide to Drosophila genes and their role in development
  • includes information on biochemical pathways
Wnt Signaling Pathway (Stanford University Medical Center)
  • resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, methods and various other items
Yeast Pathways in the Comprehensive Yeast Genome Database (MIPS)


APID (Cancer Research Center)
  • Agile Protein Interaction DataAnalyzer
  • interactive web-tool
  • all known experimentally validated protein-protein interactions
eFsite (Osaka University)
  • Electrostatic surface of Functional-SITE
  • database for molecular surfaces of proteins functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites
Expression Profiler (European Bioinformatics Institute)
  • explores protein interaction data using expression data
FunSimMat (Max Planck Institute for Informatics)
  • Functional Similarity Matrix
  • comprehensive resource of semantic and functional similarity values
IntAct Project (EMBL-EBI)
  • database and toolkit for the storage, presentation and analysis of protein interactions
InterPreTS (EMBL)
  • INTERaction PREdiction through Tertiary Structure
InterProSurf (University of Texas Medical Branch)
  • web server for predicting the functional sites on protein surfaces
InterViewer (Inha University)
  • visualization of large-scale protein interaction networks
iSPOT (Universita di Roma)
  • prediction of protein-protein interactions mediated by families of peptide recognition modules
Medusa (EMBL)
  • interface to the STRING protein interaction database
  • a general graph visualization tool
PathBLAST (Whitehead Institute)
  • network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution
  • Protein Extraction, Description, and Analysis Tool
  • exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools
PDBSiteScan (Institute of Cytology and Genetics SBRAS)
  • designed for searching 3D protein fragments similiar in structure to known active, binding and posttranslational modification sites
PIMRiderTM (Hybrigenics)
  • Hybrigenics functional proteomic software and interaction data
PIMWalkerTM (Hybrigenics)
  • a free protein-protein interaction map java viewer
PIVOT (Tel Aviv University)
  • Protein Interactions VisualizatiOn Tool
ProFace (Department of Biochemistry, Bose Institute)
  • server for the analysis of the physicochemical features of protein-protein interfaces
  • suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits
Protein3D Home (LECB)
PROTORP (University of Sussex)
  • protein-protein interface analysis server
  • analyse the properties of interfaces in the 3D structures of protein-protein associations
SCOWLP (TU Dresden)
  • Structural Characterization Of Water, Ligands and Proteins
  • web-based relational database describing PDB interface interactions at atom, residue and domain level
SPIN-PP Server (Columbia University)
  • Surface Properties of INterfaces - Protein Protein interfaces
  • database of all protein-protein interactions in the Protein Data Bank
  • Search Tool for the Retrieval of INteracting Genes/proteins
  • database of known and predicted protein-protein interactions for a large number of organisms
  • interactions include direct (physical) and indirect (functional) associations
  • data are derived from four sources: genomic context, high-throughput experiments, (conserved) coexpression and previous knowledge
YETI (University Edinburgh)
  • Yeast Exploration Tool Integrator
  • workbench tool for visualization/analysis of post-genomic data sets available for Saccharomyces cerevisiae



Modular Protein Domains
Giovanni Cesareni, Mario Gimona, Marius Sudol and Michael Yaffe
524 pp., Wiley-VCH, January 2005
ISBN: 978-3527308132 [Amazon]

Protein Modules and Protein-Protein Interactions, Volume 61 (Advances in Protein Chemistry)
Joel Janin
333 pp., Academic Press, November 2002
ISBN: 978-0120342617 [Amazon]

Protein-Protein Recognition
Colin Kleanthous
314 pp., Oxford University Press, January 2001
ISBN: 978-0199637607 [Amazon]

Proteomics and Protein-Protein Interactions : Biology, Chemistry, Bioinformatics, and Drug Design (Protein Reviews)
Gabriel Waksman
324 pp., Springer, December 2005
ISBN: 978-0387245317 [Amazon]

Proteomics in Drug Research
Michael Hamacher, Katrin Marcus, Kai Stühler, Andre van Hall, Bettina Warscheid and Helmut E. Meyer
383 pp., Wiley-VCH, May 2006
ISBN: 978-3527312269 [Amazon]

   The Jena Protein-Protein Interaction Website