LIGAND: chemical database for enzyme reactions
LIGAND: chemical database for enzyme reactions
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DOI：
10.1093/bioinformatics/14.7.591
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发表时间：
1998-01-01
期刊：
影响因子：
5.8
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Goto, S;Nishioka, T;Kanehisa, M
动机：现有的分子生物学数据库集中于生物大分子（即DNA、RNA和蛋白质）的序列和结构方面。然而，为了了解功能方面，计算这些分子的相互作用是必不可少的。此外，活细胞还含有其他分子，如代谢化合物和金属离子，这些分子也可能是生命的基本组成部分，但在公共数据库中没有很好的组织。LIGAND化学数据库是我们解决这些问题的尝试，至少对于酶促反应来说是这样。酶和化合物。酶部分是先前研究的延伸（Suyama等人，Comput.应用生物科学，9，9-15，1993），并且它是3303种酶和2976种酶促反应的平面文件表示，其化学方程式格式可由机器解析。新建立了化合物部分，用于提供有关化合物的命名和化学结构的信息。它含有5383种化合物。ENZYME和COMPOUND条目都包含丰富的交叉引用信息，其中大部分是由DBGET/LinkDB系统自动生成的，从而提供了化学和生物数据库之间的链接。LIGAND每天更新，与KEGG代谢途径数据库紧密结合，并形成了重建和计算途径的基础。可用性：LIGAND可以通过日本GenomeNet数据库服务中的DBGET/LinkDB和KEGG系统访问，网址为http://www.genome.ad.jp/。LIGAND数据库的平面文件格式可通过匿名FTP经由frp：//kegg.genome.adjp/molecules/ligand/下载。联系人：后藤@kuicr：kyoto-u.ac.jp; nishioka@scl.kyoto-u.ac.jp; kanehisa@kuicr：京都。
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 consider-ed 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 I ich 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 frp ://kegg.genome.adjp/molecules/ligand/.Contact: goto@kuicr:kyoto-u.ac.jp; nishioka@scl.kyoto-u.ac.jp; kanehisa@kuicr:kyoto-u.ac.jp.