title: EzCatDB: the enzyme reaction database, 2015 update.
abstract: The EzCatDB database (http://ezcatdb.cbrc.jp/EzCatDB/) has emphasized manual classification of enzyme reactions from the viewpoints of enzyme active-site structures and their catalytic mechanisms based on literature information, amino acid sequences of enzymes (UniProtKB) and the corresponding tertiary structures from the Protein Data Bank (PDB). Reaction types such as hydrolysis, transfer, addition, elimination, isomerization, hydride transfer and electron transfer have been included in the reaction classification, RLCP. This database includes information related to ligand molecules on the enzyme structures in the PDB data, classified in terms of cofactors, substrates, products and intermediates, which are also necessary to elucidate the catalytic mechanisms. Recently, the database system was updated. The 3D structures of active sites for each PDB entry can be viewed using Jmol or Rasmol software. Moreover, sequence search systems of two types were developed for the EzCatDB database: EzCat-BLAST and EzCat-FORTE. EzCat-BLAST is suitable for quick searches, adopting the BLAST algorithm, whereas EzCat-FORTE is more suitable for detecting remote homologues, adopting the algorithm for FORTE protein structure prediction software. Another system, EzMetAct, is also available to searching for major active-site structures in EzCatDB, for which PDB-formatted queries can be searched.
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan n.nagano@aist.go.jp.
authors.forename: Nozomi
authors.initials: N
authors.lastname: Nagano
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Naoko
authors.initials: N
authors.lastname: Nakayama
authors.affiliation: Level Five Co. Ltd., Grove Tower 4112, 4-21-1, Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Ikeda
authors.affiliation: Level Five Co. Ltd., Grove Tower 4112, 4-21-1, Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Fukuie
authors.affiliation: Level Five Co. Ltd., Grove Tower 4112, 4-21-1, Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Kiyonobu
authors.initials: K
authors.lastname: Yokota
authors.affiliation: Level Five Co. Ltd., Grove Tower 4112, 4-21-1, Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Takuo
authors.initials: T
authors.lastname: Doi
authors.affiliation: Faculty of Science and Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Kato
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Tomii
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D020407:Internet; D020539:Sequence Analysis, Protein
chemical_list: D004798:Enzymes