Networks & Interactions, Pathways and Enzymes

These links include tools and resources for enzyme, metabolic and proteomic pathways and networks. Many of these resources contain dynamic pathway diagrams. Protein-protein interactions are also represented here.

Found 182 links

Displaying 15 links

ANCHORTool Content

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ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

APIDTool Content

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Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.

links directory index: 88
TitlePublication YearGoogle Scholar Citation Count
APID: Agile Protein Interaction DataAnalyzer200688

BabelomicsTool Content

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Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

Bacteriome.orgDatabase Content

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A database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Tools are provided which allow the user to select and visualize functional, evolutionary and structural relationships between groups of interacting proteins and to focus on genes of interest.

BIOBASE Gene Regulation databasesDatabase Content

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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.

BioCartaTool Content

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

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

BioCyc Knowledge LibraryDatabase Content

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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; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

links directory index: 592
TitlePublication YearGoogle Scholar Citation Count
The MetaCyc Database2002186
The EcoCyc Database2002406

BiologicalNetworksTool Content

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BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.


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