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The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Open accessAbstract
MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways derived from more than 60 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in BioCyc.org and other genomic portals. This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1. Some of the topics that received intensive curation during this period include cobamides biosynthesis, sterol metabolism, fatty acid biosynthesis, lipid metabolism, carotenoid metabolism, protein glycosylation, antibiotics and cytotoxins biosynthesis, siderophore biosynthesis, bioluminescence, vitamin K metabolism, brominated compound metabolism, plant secondary metabolism and human metabolism. Other additions include modifications to the GlycanBuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, improvements in the PathoLogic component of Pathway Tools, and the optional addition of regulatory information to pathway diagrams.
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
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Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1000 · Cited by 9,726
Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1074 · Cited by 8,056
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Cirstea, M. S., Yu, A. C., Golz, E., Sundvick, K., Kliger, D., Radisavljevic, N., Foulger, L. H., Mackenzie, M., Huan, T., Finlay, B. B., et al. (2020) · Movement Disorders · doi:10.1002/mds.28052 · Cited by 326
A general model to predict small molecule substrates of enzymes based on machine and deep learning
Kroll, A., Ranjan, S., Engqvist, M. K. M., & Lercher, M. J. (2023) · Nature Communications · doi:10.1038/s41467-023-38347-2 · Cited by 193
Metadata
- Authors
- Caspi, R., Billington, R., Keseler, I. M., Kothari, A., Krummenacker, M., Midford, P. E., Ong, W. K., Paley, S., Subhraveti, P., & Karp, P. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-10-05
- Volume
- 48
- Issue
- D1
- Pages
- D445-D453
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2977870980
- Cited by
- 1,395
- References
- 1
- FWCI
- 27.64
- Type
- journal article
- Language
- en
- Open access
- gold
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- Caspi, R., Billington, R., Keseler, I. M., Kothari, A., Krummenacker, M., Midford, P. E., Ong, W. K., Paley, S., Subhraveti, P., & Karp, P. D. (2020). The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz862
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
