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EzCatDB specifications


Unique identifier OMICS_06070
Name EzCatDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline Nozomi Nagano

Publications for EzCatDB

EzCatDB citations


Biocuration in the structure–function linkage database: the anatomy of a superfamily

PMCID: 5467563
PMID: 28365730
DOI: 10.1093/database/bax006

[…] g. Pfam (), UniProtKB (), InterPro (), TIGRFAMs () and PANTHER () to name but a few), or a structure-centric approach [e.g. CATH () and SCOP ()] or a function-centric approach [e.g. CSA (), MACiE (), EzCatDB ()]. The SF approach integrates sequence, structure, and function as classification criteria, enhancing our abilities to discern new connections and features that help us better understand enz […]


From sequence to enzyme mechanism using multi label machine learning

BMC Bioinformatics
PMCID: 4229970
PMID: 24885296
DOI: 10.1186/1471-2105-15-150

[…] hanisms existing in nature. And only 540 proteins have been annotated with a specific MACiE mechanism. Additionally, most mechanisms only have one protein exemplar annotated within the MACiE, SFLD or EzCatDb databases, and cannot therefore be used for cross-validation.Further validation will be needed when the dataset has grown, to clarify whether the best and fastest method remains the one we ide […]


Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

PLoS One
PMCID: 3885575
PMID: 24416252
DOI: 10.1371/journal.pone.0084623

[…] te and ligand binding residue positions from the literature and structural information: We obtained the literature information about active site residues from the Enzyme Catalytic-Mechanism Database (EzCatDB, ver. 20100722) and the Catalytic Site Atlas (CSA, ver. 2.2.12) database. All annotations in the EzCatDB and the original, hand-annotated entries derived from the primary literature in the C […]


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EzCatDB institution(s)
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, Tokyo, Japan; Level Five Co Ltd, Shibaura, Minato-ku, Tokyo, Japan; Faculty of Science and Engineering, Gunma University, Kiryu, Gunma, Japan; Center for Informational Biology, Ochanomizu University, Bunkyo-ku, Tokyo, Japan
EzCatDB funding source(s)
Supported by the Institute for Bioinformatics Research and Development (BIRD), which were organized by the Japan Science and Technology Agency (JST); a Grant-in-Aid for Publication of Scientific Research Results [238048, 248047], organized by the Japan Society for the Promotion of Science (JSPS); and the Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI), Japan.

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