More information XML output
| 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. |
| Keyword |
Under investigation
|
| 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) | 3 |
| Last date of updates (date of confirmation) | 2011/12/28 (2011/12/29) |
| 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. |
| 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 |