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Relating project

Name EzCatDB
Aliases None
Description The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, and catalytic mechanisms.
Type DB
Main Institutes of management Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
Country of the Institute Japan
URL of the site http://mbs.cbrc.jp/EzCatDB/
Interface GUI
Input example Input the enzyme name in the "Enzyme Name in KEGG" box on the Search Page, then push “Search” button.
Amount of the all data for download（Mbyte） | Method to obtain the all data. 0 | currently not available
External resources (databases) in building the product. SWISS-Prot | PDB | PubMed | KEGG | CATH | PDBsum | CSA | MACiE | journal
Data type Protein-structure Enzyme
Biological species in the main concern All species
Conditions of use Attribution&Noncommercial&Share Alike User account is not required
Frequency of updates (in last two years) 1 time/month
Last date of updates (date of confirmation) 2010/08/19 (2010/08/26)
Main IDs used in the products DB code (酵素ID) | EC number | PDB ID | CATH code | KEGG | UniProt ID | PubMed ID
How to make a link to get access to each IDs. http://mbs.cbrc.jp/EzCatDB/search/get.do?dbcode=[DB code]
external databases to which this database/tool have links SWISS-Prot | PDB | PubMed | KEGG | CATH | PDBsum | PDBj | CSA | MACiE
Published papers (PubMed IDs) Nozomi Nagano, Tamotsu Noguchi, Yutaka Akiyama (2007) "Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database." PROTEINS: Structure, Function, and Bioinformatics. 66, 147-159. | Nozomi Nagano (2005) "EzCatDB: The Enzyme Catalytic-Mechanism Database." Nucleic Acids Research, 33, Database Issue, D407-D412.

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Project name BIRD/Japan Science and Technology Corporation (JST)
Area Genome Informatics
Purpose a novel classification of enzyme catalytic mechanisms has been proposed. In this project, we are trying to develop a system to predict enzyme reactions based on the enzyme reaction classification.
Introduction In this project, we are trying to develop a system to predict enzyme functions, that is reactions, using machine learning and enzyme reaction classification.
Keyword Enzyme | reaction
Patent (Japan, overseas) Under investigation
Product (Database, Tool) Nothing