Nucleic Acids Research, 2005, Vol. 33, Database issue D407-D412
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
EzCatDB: the Enzyme Catalytic-mechanism Database
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan and PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi-shi, Saitama 332-0012, Japan
* Tel: +81 3 3599 8043; Fax: +81 3 3599 8081; Email: n.nagano{at}aist.go.jp
Received August 15, 2004; Revised and Accepted October 8, 2004
The EzCatDB (Enzyme Catalytic-mechanism Database) specifically includes catalytic mechanisms of enzymes in terms of sequences and tertiary structures of enzymes, and proposed catalytic mechanisms, along with ligand structures. The EzCatDB groups enzyme data in the Protein Data Bank (PDB) and the SWISS-PROT database with identical domain compositions, Enzyme Commission (EC) numbers and catalytic mechanisms. The EzCatDB can be queried by the type of catalytic residue, name and type of ligand molecule that interacts with an enzyme as a cofactor, substrate or product. It can provide literature information, other database codes and EC numbers. The EzCatDB provides ligand annotation for enzymes in the PDB as well as literature information on structure and catalytic mechanisms. Furthermore, the EzCatDB also provides a hierarchic classification of catalytic mechanisms. This classification incorporates catalytic mechanisms and active-site structures of enzymes as well as basic reactions and reactive parts of ligand molecules. The EzCatDB is available at http://mbs.cbrc.jp/EzCatDB/.
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