The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
Open accessAbstract
Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.
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The carbohydrate-active enzymes database (CAZy) in 2013
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The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
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Self-citationdbCAN: a web resource for automated carbohydrate-active enzyme annotation
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Self-citationYou are what you eat: Diet, health and the gut microbiota
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Research works printed but not linked: 1
- Hobbs, 2021, Microbiology Society Annual Conference 2021
Cited by
Andreu-Sánchez, S., Blanco-Míguez, A., Wang, D., Golzato, D., Manghi, P., Heidrich, V., Fackelmann, G., Zhernakova, D. V., Kurilshikov, A., Valles-Colomer, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.014 · Cited by 81
Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.007 · Cited by 17
Genomic and functional diversity of the human-derived isolates of Faecalibacterium
Li, W., Lin, X., Liang, H., Wu, Z., Wang, M., Sun, J., Li, X., He, W., Gao, X., Hu, T., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1379500 · Cited by 17
Wimmer, B. H., Moraïs, S., Amit, I., Tovar-Herrera, O., Tatli, M., Trautwein-Schult, A., Pfister, B., Zalk, R., Tödtli, P., Simoni, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65800-1 · Cited by 15
Plant-associated fungi co-opt ancient antimicrobials for host manipulation
Mesny, F., Wolf, V., López-Moral, A., Kraege, A., Punt, W., Liu, S., Zhu, J., Park, J., Sato, Y., & Thomma, B. P. H. J. (2026) · Science Advances · doi:10.1126/sciadv.aec1406 · Cited by 11
Metadata
- Authors
- Zheng, J., Ge, Q., Yan, Y., Zhang, X., Huang, L., & Yin, Y.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-05-01
- Volume
- 51
- Issue
- W1
- Pages
- W115-W121
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4367598489
- Cited by
- 1,084
- References
- 34
- FWCI
- 81.89
- Type
- journal article
- Language
- en
- Open access
- gold
- Funders
- National Institutes of Health (R01GM140370, R21AI171952)
- National Science Foundation (DBI-1933521)
- United States Department of Agriculture (58-8042-9-089)
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- Zheng, J., Ge, Q., Yan, Y., Zhang, X., Huang, L., & Yin, Y. (2023). dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad328
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