Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.genome.ad.jp/ligand
Full name: database of chemical compounds and reactions in biological pathways
Description: KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RCLASS, and ENZYME databases, whose entries are identified by C, G, R, RC, and EC numbers, respectively. ENZYME is derived from the IUBMB/IUPAC Enzyme Nomenclature with annotation of reactions and sequences.
Year founded: 1998
Last update: 2017-11-02
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Country/Region: Japan
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Contact information

University/Institution: Kyoto University
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Country/Region: Japan
Contact name (PI/Team): Susumu Goto
Contact email (PI/Helpdesk): goto@kuicr.kyoto-u.ac.jp

Publications

11752349
LIGAND: database of chemical compounds and reactions in biological pathways. [PMID: 11752349]
Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M.

LIGAND is a composite database comprising three sections: COMPOUND for the information about metabolites and other chemical compounds, REACTION for the collection of substrate-product relations representing metabolic and other reactions, and ENZYME for the information about enzyme molecules. The current release (as of September 7, 2001) includes 7298 compounds, 5166 reactions and 3829 enzymes. In addition to the keyword search provided by the DBGET/LinkDB system, a substructure search to the COMPOUND and REACTION sections is now available through the World Wide Web (http://www.genome.ad.jp/ligand/). LIGAND may be also downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand/).

Nucleic Acids Res. 2002:30(1) | 131 Citations (from Europe PMC, 2021-06-19)
10592281
LIGAND: chemical database of enzyme reactions. [PMID: 10592281]
Goto S, Nishioka T, Kanehisa M.

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 reconstruction of metabolic pathways in the completely sequenced organisms. The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html ) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad.jp/molecules/ligand/ ).

Nucleic Acids Res. 2000:28(1) | 23 Citations (from Europe PMC, 2021-06-19)
9847234
LIGAND database for enzymes, compounds and reactions. [PMID: 9847234]
Goto S, Nishioka T, Kanehisa M.

LIGAND is a composite database consisting of three sections and containing the information of chemical substances, chemical reactions and enzymes that catalyze reactions. The COMPOUND section is a collection of metabolic compounds, as well as macromolecules, chemical elements and other chemical substances in a living cell. The ENZYME section is a collection of all known enzymatic reactions, together with the information of enzyme molecules, classified according to the EC (Enzyme Commission) numbers. The REACTION section is a new addition to the database containing metabolic reactions that appear in the pathway diagrams of the KEGG/PATHWAY database and/or in the ENZYME section. The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad. jp/molecules/ligand).

Nucleic Acids Res. 1999:27(1) | 5 Citations (from Europe PMC, 2021-06-19)
9730924
LIGAND: chemical database for enzyme reactions. [PMID: 9730924]
Goto S, Nishioka T, Kanehisa M.

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: goto@kuicr.kyoto-u.ac.jp; nishioka@scl.kyoto-u.ac.jp; kanehisa@kuicr.kyoto-u.ac.jp

Bioinformatics. 1998:14(7) | 44 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
942/5061 (81.407%)
Pathway:
57/349 (83.954%)
942
Total Rank
203
Citations
8.826
z-index

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Record metadata

Created on: 2018-02-08
Curated by:
huma shireen [2018-09-04]
Zhuang Xiong [2018-02-27]