Bioinformatics Links Directory : Interactions, Pathways, Enzymes

These links include databases for enzyme, metabolic and proteomic pathways. Many of these resources contain dynamic pathway diagrams.

WebInterViewer - (Found July 2, 2008 )

WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.
http://interviewer.inha.ac.kr/

Pathway Hunter Tool - (Found July 2, 2008 )

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.
http://www.pht.uni-koeln.de

PathBLAST - (Found July 2, 2008 )

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.
http://www.pathblast.org/

Path-A - (Found July 2, 2008 )

Pathway Analyst (Path-A) predicts and annotates pathways present in the query organism and provides a browsable database of ten currently supported metabolic pathways. Path-A can also take as input a list of protein sequences and identify those sequences that are likely to participate in the supported metabolic pathways.
http://path-a.cs.ualberta.ca/

MINT - a Molecular INTeractions database - (Found July 2, 2008 )

Curated database with a focus on experimentally verified molecular interaction data collected from scientific literature. Emphasis on mammalian organisms.
http://cbm.bio.uniroma2.it/mint/

metaSHARK - (Found July 2, 2008 )

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.
http://bioinformatics.leeds.ac.uk/shark/

MetaPath Online - (Found July 2, 2008 )

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.
http://scopes.biologie.hu-berlin.de/

Metabolic PathFinding - (Found July 2, 2008 )

The Metabolic PathFinding website takes a source and a target metabolic node as input and finds the shortest path between them in a graph based on the reactions and compounds from the KEGG LIGAND database. Various types of input can be provided, including LIGAND database identifiers and EC numbers. The web tool employs two selectable methods to filter out pathways going through highly connected compounds such as water .
http://www.scmbb.ulb.ac.be/pathfinding/

KOBAS - (Found July 2, 2008 )

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occuring (or significantly enriched) pathways among the queried sequences compared against a background distribution.
http://kobas.cbi.pku.edu.cn

KEGG: Kyoto Encyclopedia of Genes and Genomes - (Found July 2, 2008 )

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 cellular processes), and LIGAND (chemical compounds and chemical reactions).
http://www.genome.ad.jp/kegg/