The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37,000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA.
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Tomer
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Altman
Richard
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Billington
Kate
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Dreher
Hartmut
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Foerster
Carol A
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Fulcher
Timothy A
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Holland
Ingrid M
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Keseler
Anamika
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Kothari
Aya
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Kubo
Markus
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Krummenacker
Mario
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Latendresse
Lukas A
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Mueller
Quang
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Ong
Suzanne
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Paley
Pallavi
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Subhraveti
Daniel S
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Weaver
Deepika
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Weerasinghe
Peifen
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Zhang
Peter D
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Karp
D062126:Databases, Chemical; D004798:Enzymes / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D063990:Gene Ontology; D016678:Genome; D020407:Internet; D007700:Kinetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D011134:Polysaccharides / Q000378:metabolism; D012984:Software
D004798:Enzymes; D011134:Polysaccharides