| 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 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)
|
| DIP (UCLA) |
- 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
|
| IBIS (NCBI) |
- 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 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
- VirusMint - Virus protein interactions database
|
| 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 250 bacterial species/strains
|
| MPPI (MIPS) |
- 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)
|
| PINT (bioinfodatabase.com) |
- 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
|
| SPiD (INRA) |
- 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) |
| YPD™ (BIOBASE) |
- Yeast Proteome Database
- comprehensive knowledge resource for the proteins of S. cerevisiae
|
| ADAN (EMBL) |
- 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
|
| PRIMOS (BIOMIS, FH Hagenberg) |
- 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
|
| 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) |
- 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
|
| 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)
|
| 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
|
| 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
|
| 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
|
| 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
- integrated database for genetic information and signal transduction systems
|
| 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) |
- 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
|
| PEDANT (GSF) |
- 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
|
| 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
|
The Jena Protein-Protein Interaction Website 