LIGAND: chemical database for enzyme reactions
نویسندگان
چکیده
MOTIVATION The existing molecular biology databases focus on the sequence and structural aspects of biological macromolecules, i.e. DNAs, RNAs and proteins. However, in order to understand the functional aspects, it is essential to computerize the interaction of these molecules. Furthermore, living cells contain additional molecules, such as metabolic compounds and metal ions, that may also be considered as parts of the basic building blocks of life, but are not well organized in public databases. LIGAND chemical database is our attempt to solve these problems, at least for enzymatic reactions. RESULTS LIGAND consists of two sections: ENZYME and COMPOUND. The ENZYME section is an extension of previous studies (Suyama et al. , Comput. Applic. Biosci., 9, 9-15, 1993), and it is a flat-file representation of 3303 enzymes and 2976 enzymatic reactions in the chemical equation format that can be parsed by machine. The COMPOUND section has been newly constructed for information on the nomenclature and chemical structures of compounds. It contains 5383 chemical compounds. Both ENZYME and COMPOUND entries contain rich cross-reference information, most of which is automatically generated by the DBGET/LinkDB system, thus providing the linkage between chemical and biological databases. LIGAND is updated daily, tightly coupled with the KEGG metabolic pathway database, and forms the basis for reconstruction and computation of pathways. AVAILABILITY LIGAND can be accessed through the DBGET/LinkDB and KEGG systems in the Japanese GenomeNet database service via http://www.genome.ad.jp/. The flat-file format of the LIGAND database can be downloaded by anonymous FTP via ftp://kegg. genome.adjp/molecules/ligand/. CONTACT [email protected]; [email protected]; [email protected]
منابع مشابه
LIGAND: chemical database of enzyme reactions
LIGAND is a composite database comprising three sections: ENZYME for the information of enzyme molecules and enzymatic reactions, COMPOUND for the information of metabolites and other chemical compounds, and REACTION for the collection of substrate-product relations. The current release includes 3390 enzymes, 5645 compounds and 5207 reactions. The database is indispensable for the reconstructio...
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ورودعنوان ژورنال:
- Bioinformatics
دوره 14 7 شماره
صفحات -
تاریخ انتشار 1998