| AllFuse (European Bioinformatics Institute) |
- functional association of proteins in complete genomes (unavailable ??)
|
| ASEdb |
- Alanine Scanning Energetics DataBase
- database of hotspots in 3D protein structures
|
| Bacteriome.org (University of Toronto) |
- bacterial protein interaction database
- database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase
|
| BID (A & M University Texas) |
- Binding Interface Database
|
| 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
|
| DIP (UCLA) |
- Database of Interacting Proteins
|
| Drosophila Protein Interaction Map (PIM) Database (Wayne State University) |
| EchoBASE (University of York) |
- integrated post-genomic database for E. coli
|
| Genomic Knowledge Database (RIKEN, Institute of Physical and Chemical Research) |
- integrates various types of biological and biomedical databases in order to discover disease-related cascades and medicinal target candidates
|
| 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
|
| ICBS (University of California) |
- Inter-Chain Beta-Sheets database
- protein-protein interactions mediated by interchain ß-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
|
| molmovdb.org (Yale University) |
- database of macromolecular movements
|
| MPact (MIPS) |
|
| MPIDB (J. Craig Venter Institute) |
- Microbial Protein Interaction DataBase
- provide all known physical microbial interactions
- experimentally determined interactions among proteins of 191 bacterial species/strains
|
| MPPI (MIPS) |
- Mammalian Protein-Protein Interaction database
|
| NetPro (Molecular Connections) |
- database of protein-protein and protein-small molecules interaction
|
| PathCalling Yeast Interaction Database (University of Washington, Curagen Corp.) |
| PDZBase (Weill Medical College of Cornell University) |
- manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains
|
| PepCyber: P~PEP (University of Minnesota) |
- database of human protein-protein interactions mediated by phosphoprotein binding domains (PPBDs)
|
| 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 Interactions and Molecular Information databasE
- integrated gene/protein informatics database based on natural language processing
|
| ProtoArray® (Invitrogen) |
| ProMesh (University of Queensland) |
- protein-protein interaction database [restricted]
|
| Protein Interaction Database (Protein Lounge) |
- database lists thousands of human protein-protein interactions
- created through in-dept research of hundreds of signal transduction pathways
|
| Protein Interaction Maps - PIMs (Hybrigenics) |
- functional proteomics software platform, dedicated to the exploration of protein pathways
- PIM's available for Helicobacter pylori, Hepatitis C Virus, 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]
|
| Protein-Protein Interaction Viewer [+ FANTOM2 Viewer] (RIKEN Yokohama Institute) |
| PSIbase (BioSystems Dept., KAIST & BiO centre) |
- structural interactome map of all proteins
|
| Repair-FunMap (Temple University) |
- database that provides the functional networking of proteins related to DNA repair processes in the cell
- capable of generating functional maps of interacting proteins around a protein of interest
|
| SNAPPIView (University of Dundee) |
- Structures, iNterfaces and Alignments for Protein-Protein Interactions
- object-oriented database of domain-domain interactions observed in structural data
|
| SPIN-PP Server (Columbia University) |
- Surface Properties of INterfaces - Protein Protein interfaces
- database of all protein-protein interactions in the PDB
|
| Yeast Interacting Proteins Database (Kanazawa University) |
|
| Yeast Protein Linkage Map Data (University of Washington) |
| YPD™ (BIOBASE) |
- Yeast Proteome Database
- comprehensive knowledge resource for the proteins of S. cerevisiae
|
| ADAN (EMBL) |
- prediction of protein-protein
interAction of moDular domAiNs
|
| AtPID (Northeast Forest University) |
- Arabidopsis Thaliana Protein Interactome Database
- rich source of information for system-level understanding of gene function and biological processes in A. thaliana
- integrates data from several bioinformatics prediction methods and manually collected information from the literature
- contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation
|
| E. Coli Predicted Protein Interactions Database (Universidad Autónoma Cantoblanco) |
- in silico two-hybrid system for the prediction of interaction partners to the entire E. coli genome
|
| Fly-DPI ( National Health Research Institutes) |
- statistical model to predict protein interaction networks of Drosophila melanogaster
|
| 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
|
| HPID (Inha University) |
- Human Protein Interaction Database
|
| ICBS (University of California) |
- Inter-Chain Beta-Sheets
- database of protein-protein interactions mediated by interchain ß-sheet formation
|
| 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
|
| InterProSurf (University of Texas Medical Branch) |
- web server
- predicts interacting amino acid residues in proteins that are most likely to interact with other proteins
|
| meta-PPISP (Florida State University) |
- meta web server for protein-protein interaction site prediction
|
| NOXclass (Max-Planck-Institut für Informatik) |
- SVM (support vector machine algorithm) classifier identifying protein-protein interaction types
|
| OPHID (Ontario Cancer Institute & University of Toronto) |
- Online Predicted Human Interaction Database
- designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks
|
| PIBASE (University of California) |
- comprehensive database of structurally defined interfaces between pairs of protein domains
|
| 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 44 microorganisms
|
| PreSPI (Information and Communications University) |
- PREdiction System for Protein Interaction
- domain combination based protein interaction prediction system
|
| PRIMOS (BIOMIS, FH Hagenberg) |
- PRotein Interaction and MOlecule Search) database
- integrated knowledge portal for analysing integrated protein-protein interaction data
|
| PRISM (Koc University) |
- PRotein Interactions by Structural Matching
- explore protein interfaces and predict protein-protein interactions
|
| PRODISTIN Web Site (LGPD/IBDM, CNRS) |
- 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) |
- database of predicted protein-protein interaction network in yeast
- 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
|
| BioCarta (BioCarta) |
- charting pathways of life
|
| BioCyc (SRI) |
- includes the literature-derived pathway/genome databases Ecocyc (encyclopedia of E. coli genes and metabolism) & MetaCyc (metabolic pathways and enzymes from 150 species) as well as computationally derived genome/pathway databases for 12 species
|
| BN++ (Center for Bioinformatics Saar & Center for Bioinformatics Tübingen) |
- biochemical network library for analyzing and visualizing complex biochemical networks and processes
|
| CSNDB (NIHS) |
- Cell Signaling Networks DataBase
|
| 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)
|
| DIMA (MIPS, TUM) |
- 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
|
| DOQCS (NCBS) |
- 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
|
| InCeP (Kazusa DNA Research Institute) |
- database for IntraCellular Pathway based on mKIAA protein-protein interactions
|
| InterDom (Laboratories for Information Technology) |
- database of putative INTERacting protein DOMains derived from multiple sources
|
| KEGG |
|
| KEGG LIGAND |
- 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
|
| Pathway Database (Protein Lounge) |
- database of protein signaling and metabolic pathways
|
| 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
|
| PUMA2 (Argonne National Lab) |
- evolutionary analysis of metabolism
|
| Roche Applied Science 'Biochemical Pathways' |
| SCOPPI (TU Dresden) |
- Structural Classification Of Protein-Protein Interfaces
|
| SCOWLP (BIOTEC TU Dresden) |
- 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
|
| SoyBase (Yale University) |
|
| TRANSCompel (BIOBASE) |
- database of composite regulatory elements affecting gene transciption in eukaryotes [Guided Tour]
|
| TRANSPATH (BIOBASE) |
- 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) |
| Yeast Interactome (Boston University) |
- interaction map with valuable information regarding to biochemical processes
|
| 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
|
| ADVICE (Institute for Infocomm Research) |
- Automated Detection and Validation of Interaction by Co-Evolution
- prediction and validation of protein-protein interactions
|
| BioLayout Java (EMBL) |
- automatic graph layout algorithm for similarity and network visualization
|
| 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 functional similarity database
|
| IntAct Project (European Bioinformatics Institute) |
- database and toolkit for the storage, presentation and analysis of protein interactions
|
| InterPreTS (EMBL) |
- protein 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
|
| InterWeaver (Institute for InfoComm Research) |
- web server of interaction reports
|
| iPPI (National Bioinformatics Center Cuba) |
- infers protein-protein interactions through homology search
|
| IPPRED (Centre de Bioinformatique de Bordeaux) |
- proteins interactions inference server
- infers interactions through homology search
|
| 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
|
| NetAlign (Lab of Protein Crystallography, USTC) |
- a web-based tool for comparison of protein interaction networks
|
| 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
|
| PEDANT (GSF) |
- Protein Extraction, Description, and Analysis Tool
|
| 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) |
| Protein-Protein Interaction Server (University College London) |
|
| 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
|
| STRING (EMBL) |
- 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
|
Protein-Protein Interaction Website