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- person_outline Nozomi Nagano
Publications for EzCatDB
Biocuration in the structure–function linkage database: the anatomy of a superfamily
[…] 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
[…] 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
[…] 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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