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LIGAND

http://www.genome.ad.jp/ligand/

Goto, S.1, Okuno, Y.1, Hattori, M.1, Nishioka, T.2, Kanehisa, M.1

1Institute for Chemical Research, Kyoto University
2Graduate School of Agricultural Sciences, Kyoto University

Contact   goto@kuicr.kyoto-u.ac.jp


Database Description

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 enzymatic and other reactions, and ENZYME for the information about enzyme molecules. The current release (as of September 7, 2001) includes 7,298 compounds, 5,166 reactions, and 3,829 enzymes. 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/ligand/) or may be downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand).

Recent Developments

The COMPOUND and REACTION sections are now managed by the ISIS/HOST database. They can be accessed through the Chemscape server, which enables users to search by compound structures via web browsers if Chime plug-in and ISIS/Draw are installed on the client machine. Both are freely available from the MDL web site (http://www.mdli.com/). The COMPOUND section has been originally created by extracting chemical compounds from the metabolic pathways of the KEGG/PATHWAY database, as well as the ENZYME section of LIGAND. The current version of COMPOUND includes chemical compounds related to drugs and environmental pollutants as well, and their ratio is increasing. They will be used, for example, as the starting compounds to search possible degradation pathways, which will connect to the existing pathways presented in the KEGG/PATHWAY database.

Acknowledgements

We thank Nobue Takeuchi, Tomoko Komeno, Rumiko Yamamoto and Yuriko Matsuura for inputting the compound and reaction data. This work was supported by the grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan, Japan Society for the Promotion of Science, and Japan Science and Technology Corporation. The computation time was provided by the Supercomputer Laborator, Institute for Chemical Research, Kyoto University.

REFERENCES

  1. Enzyme Nomenclature from International Union of Biochemistry and Molecular Biology. http://www.chem.qmw.ac.uk/iubmb/
  2. UM-BBD. http://umbbd.ahc.umn.edu/

Category   Metabolic Pathways and Cellular Regulation

Go to the abstract in the NAR 2002 Database Issue.

 

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