Bioinformatics Links Directory : Interactions, Pathways, Enzymes

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

IMEx - (Found July 2, 2008 )

The IMEx consortium is a group of major public interaction data providers intending to share curation effort and exchange completed records on molecular interaction data, similar to successful global collaborations for protein and DNA sequences and for macromolecular structures.
http://imex.sourceforge.net/

iMOT - (Found July 2, 2008 )

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
http://caps.ncbs.res.in/imot/iMOTserver.html

IntEnz: Integrated relational Enzyme database - (Found July 2, 2008 )

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 chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions; Swiss Institute of Bioinformatics (SIB) Enzyme Nomenclature database (ENZYME); BRENDA, the enzyme function database which contains...
http://www.ebi.ac.uk/intenz

BioCarta - (Found July 2, 2008 )

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

BIOBASE Gene Regulation databases - (Found July 2, 2008 )

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; SMARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.
http://www.gene-regulation.com/pub/databases.html

BIND - The Biomolecular Interaction Network Database - (Found July 2, 2008 )

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
http://www.bind.ca/

Argonne National Laboratory - Computational Biology Databases - (Found July 2, 2008 )

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.
http://www-unix.mcs.anl.gov/compbio/index.html

APID - (Found July 2, 2008 )

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.
http://bioinfow.dep.usal.es/apid/

ADVICE - (Found July 2, 2008 )

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 that co-evolution of proteins is useful for predicting and validating protein-protein interactions.
http://advice.i2r.a-star.edu.sg/

BioCyc Knowledge Library - (Found July 2, 2008 )

BioCyc is a collection of pathwaygenome 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)
http://www.biocyc.org/