copied from Nucleic Acids Research, 2005, Vol. 33, Database issue (link directs to table of contents with many original papers on the below mentioned databases)
return to Database resources and links

No.b Database_name___ Full_name_and/or_description_________________ URL 6. Metabolic Enzymes and Pathways; Signaling Pathways 6.1. Enzymes and Enzyme Nomenclature 421 BRENDA Enzyme names and biochemical properties http://www.brenda.uni-koeln.de 109 ENZYME Enzyme nomenclature and properties http://www.expasy.org/enzyme 459 Enzyme Nomenclature IUBMB Nomenclature Committee recommendations http://www.chem.qmw.ac.uk/iubmb/enzyme 613 EzCatDB Enzyme Catalytic Mechanism Database http://mbs.cbrc.jp/EzCatDB/ 508 IntEnz Integrated enzyme database and enzyme nomenclature http://www.ebi.ac.uk/intenz 716 PDBrtf Representation of target families of enzymes in PDB http://cgl.imim.es/pdbrtf/ 758 SCOPEC Mapping of catalytic function to domain structure http://www.enzome.com/databases/scopec.php 6.2. Metabolic Pathways 644 BioSilico Integrated access to various metabolic databases http://biosilico.kaist.ac.kr/ 112 KEGG Pathway Metabolic and regulatory pathways in complete genomes http://www.genome.jp/kegg/pathway.html 114 MetaCyc Metabolic pathways and enzymes from various organisms http://metacyc.org 115 PathDB Biochemical pathways, compounds and metabolism http://www.ncgr.org/pathdb 117 UM-BBD University of Minnesota biocatalysis and biodegradation database http://umbbd.ahc.umn.edu/ 6.3. Intermolecular Interactions and Signaling Pathways 633 3DID 3D interacting domains: domain–domain interactions in proteins with known 3D structures http://3did.embl.de 405 aMAZE A system for the annotation, management, and analysis of biochemical and signalling pathway networks http://www.amaze.ulb.ac.be/ 103 BIND Biomolecular interaction network database http://www.bind.ca 419 BioCarta Online maps of metabolic and signaling pathways http://www.biocarta.com/genes/allPathways.asp 422 BRITE Biomolecular relations in information transmission and expression, part of KEGG http://www.genome.ad.jp/brite 659 DDIB Database of domain interactions and binding http://www.ddib.org/ 104 DIP Database of interacting proteins: experimentally determined protein–protein interactions http://dip.doe-mbi.ucla.edu 105 DRC Database of ribosomal crosslinks http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc 329 GeneNet Database on gene network components http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet 664 hp-DPI Database of protein interactions in Helicobacter pylori http://dpi.nhri.org.tw/hp/ 688 HPID Human protein interaction database http://www.hpid.org/ 507 IntAct project Protein–protein interaction data http://www.ebi.ac.uk/intact 770 Inter-Chain Beta-Sheets Protein–protein interactions mediated by interchain beta-sheet formation http://www.igb.uci.edu/servers/icbs/ 510 InterDom Putative protein domain interactions http://interdom.lit.org.sg 718 PDZBase Protein–protein interactions involving PDZ domains http://icb.med.cornell.edu/services/pdz/start 749 Protein-protein interfaces Interacting residues in protein–protein interfaces in PDB http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html 773 PINdb Proteins interacting in nucleus (human and yeast) http://pin.mskcc.org/ 748 POINT Prediction of human protein–protein interactome http://point.nchc.org.tw/ 616 PSIbase Interaction of proteins with known 3D structures http://psimap.kaist.ac.kr/ 612 Reactome A knowledgebase of biological pathways http://www.reactome.org/ 571 ROSPath Reactive oxygen species (ROS) signaling pathway http://rospath.ewha.ac.kr/ 395 STCDB Signal transductions classification database http://bibiserv.techfak.uni-bielefeld.de/stcdb/ 582 STRING Predicted functional associations between proteins http://string.embl.de/ 341 TRANSPATH Gene regulatory networks and microarray analysis http://www.biobase.de/pages/products/databases.html

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.