Protein Interactions and Pathways

Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested t - [Read more ADVICE]

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available. - [Read more Argonne National Laboratory - Computational Biology Databases]

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams. - [Read more ArrayXPath]

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records. - [Read more BIND - The Biomolecular Interaction Network Database]

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database. - [Read more BIOBASE Gene Regulation databases]

Information about gene function, proteomic pathways, and reagent exchange; very clear pathway diagrams; can search for pathways by title or browse an organized list. - [Read more BioCarta]

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCy - [Read more BioCyc Knowledge Library]

Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics. - [Read more BRENDA - The Comprehensive Enzyme Information System]

CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered. - [Read more CNplot: Visualization of Pre-Clustered networks]

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimi - [Read more Cytoscape]

The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries. - [Read more DIP]

Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only. - [Read more ENZYME - Enzyme nomenclature database]

Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD). - [Read more GeneExpress2.1]

iHOP (Information Hyperlinked over Proteins) is a system that allows one to navigate through a network of genes and proteins based on the content of PubMed abstracts. For each gene search, iHOP reports sentences from abstracts associating it with other g - [Read more iHOP]

The goal of IntEnz is to create a single relational database containing enzyme data from three different sources: the official version of the Enzyme Nomenclature comprising recommendations of the Nomenclature Committee of the International Union of Bio ch - [Read more IntEnz: Integrated relational Enzyme database]

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast. - [Read more Interolog/Regulog Database]

InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners - [Read more InterWeaver]

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for - [Read more KEGG: Kyoto Encyclopedia of Genes and Genomes]

Curated database with a focus on experimentally verified molecular interaction data collected from scientific literature. Emphasis on mammalian organisms. - [Read more MINT - a Molecular INTeractions database]

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, M - [Read more MIPS]

PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user. - [Read more PathBLAST]

Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite. - [Read more Pathway Hunter Tool]

Pathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses. - [Read more Pathway Miner]

The Pathway Resource List (PRL) is a database of 150+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams, protein sequences, and protein-compound - [Read more Pathway Resource List]

Reactome is a database of human biological pathways and processes ranging from basic processes of metabolism to complex regulatory pathways. The data is curated by biologists and subsequently peer-reviewed for accuracy and consistency. Cross-references w - [Read more Reactome - a knowledgebase of biological processes]

The Restriction Enzyme Database, a collection of information about restriction enzymes and related proteins. - [Read more REBASE]

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a protein-protein interaction/association database. Both known and predicted interactions are included. The interactions are derived from existing data sources and literature and fr - [Read more STRING]

Taverna is a tool for creating and running bioinformatics workflows. - [Read more Taverna]

Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically. - [Read more The GRID - General Repository for Interaction Datasets]

Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows. - [Read more The Osprey Network Visualization System]