Goto S, Nishioka T, Kanehisa M
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
Bioinformatics. 1998;14(7):591-9. doi: 10.1093/bioinformatics/14.7.591.
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.
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.
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/.
goto@kuicr.kyoto-u.ac.jp; nishioka@scl.kyoto-u.ac.jp; kanehisa@kuicr.kyoto-u.ac.jp
现有的分子生物学数据库专注于生物大分子（即DNA、RNA和蛋白质）的序列和结构方面。然而，为了理解其功能方面，将这些分子的相互作用进行计算机化处理至关重要。此外，活细胞还包含其他分子，如代谢化合物和金属离子，它们也可被视为生命基本构建单元的一部分，但在公共数据库中并未得到很好的整理。LIGAND化学数据库就是我们为解决这些问题所做的尝试，至少针对酶促反应。
LIGAND由两部分组成：ENZYME和COMPOUND。ENZYME部分是先前研究（Suyama等人，《计算机应用于生物科学》，第9卷，第9 - 15页，1993年）的扩展，它是以化学方程式格式对3303种酶和2976个酶促反应的平面文件表示，可由机器解析。COMPOUND部分是新构建的，用于提供化合物的命名和化学结构信息。它包含5383种化学化合物。ENZYME和COMPOUND条目都包含丰富的交叉参考信息，其中大部分由DBGET/LinkDB系统自动生成，从而提供了化学数据库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耦合，并构成途径重建和计算的基础。
可通过日本GenomeNet数据库服务中的DBGET/LinkDB和KEGG系统，经由http://www.genome.ad.jp/访问LIGAND。LIGAND数据库的平面文件格式可通过匿名FTP经由ftp://kegg.genome.adjp/molecules/ligand/下载。
goto@kuicr.kyoto-u.ac.jp；nishioka@scl.kyoto-u.ac.jp；kanehisa@kuicr.kyoto-u.ac.jp
