MetaCyc

MetaCyc
Content
Description	Database of metabolic pathways and enzymes
Contact
Research center	SRI International
Authors	R. Caspi, H. Foerster, C.A. Fulcher, L.A. Mueller, P.D. Karp
Primary citation	Caspi et al. (2014)
Release date	1997
Access
Website	http://metacyc.org/

The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc data cover all domains of life and have been curated from more than 41,000 publications^[1]^[2]^[3]

MetaCyc applications include use as a reference data set for computationally predicting the metabolic pathways of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection. MetaCyc is also used in metabolic engineering and metabolomics research.

MetaCyc contains extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, in some cases, kinetic constants. MetaCyc data on reactions includes predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds. It also provides enzyme mini-reviews and literature references. MetaCyc data on metabolites includes chemical structures, predicted Gibbs free energies of formation, and links to external databases.

References

^ ^a ^b Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (January 2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases". Nucleic Acids Res. 42 (Database issue): D473–9. doi:10.1093/nar/gkp875. PMC 2808959. PMID 19850718.
^ "MetaCyc Publications".
^ Karp PD, Caspi R (September 2011). "A survey of metabolic databases emphasizing the MetaCyc family". Arch. Toxicol. 85 (9): 1015–33. doi:10.1007/s00204-011-0705-2. PMC 3352032. PMID 21523460.

[pmid24225315-1] Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (January 2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases". Nucleic Acids Res. 42 (Database issue): D473–9. doi:10.1093/nar/gkp875. PMC 2808959. PMID 19850718.

[metacyc.org-2] "MetaCyc Publications".

[pmid21523460-3] Karp PD, Caspi R (September 2011). "A survey of metabolic databases emphasizing the MetaCyc family". Arch. Toxicol. 85 (9): 1015–33. doi:10.1007/s00204-011-0705-2. PMC 3352032. PMID 21523460.

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