KEGG COMPOUND

Several authors have successfully use pharmacologically indexed databases such as the Thomson Derwent WDI [54] and the KEGG COMPOUND [55] database in which several thousand molecules are recorded according to their... 

Another resource that is useful in metabolic pathway analysis is the KEGG COMPOUND database of chemical compounds. This database is supplemented by the database of reaction information, which consists of REACTION, RPAIR, and ENZYME. The reaction formulas (chemical equations) in the ENZYME... 

This task was done by comparing the new compound first against the KEGG COMPOUND database to retrieve a list of candidate compounds that are most similar to the query. The matched compounds are then queried against the RDM pattern library to retrieve a list of putative RDM patterns. In the third step, the query compound is transformed into new possible compounds based on the retrieved transformation patterns. These newly generated compounds are then used iteratively as a new query to repeat the prediction cycle until no new transformations can be found. This approach retrieved successfully the degradation pathway for 1,2,3,4-tetrachlorobenzene (34). 

Table V shows a classification of binary relations gene-gene relations, protein-protein relations, and other molecule-molecule relations. Different sets of binary relations can then be related to different types of graphs. For example, the generalized protein-protein interaction network is equivalent to a set of protein-protein binary relations. The KEGG metabolic pathway is a generalized protein-protein network, but it is also a network of chemical compounds that can be converted to a set of com-...

The path computation has been most successful when applied to a specific class of binary relations, namely the substrate-product relations of enzymatic reactions. They constitute a well-characterized set of binary relations, and the amount of available data is relatively large. There are about 3,500 main reactions between the main compounds that are represented in the KEGG pathway diagrams. An enzymatic reaction generally involves multiple substrates and multiple products, so that it must first be decomposed into all possible substrate-product binary relations. However, because the relations involving ubiquitous compounds such as water and ATP will make many undesired connections, it is better to limit to main compounds for practical purposes. 

The KEGG (Kyoto Encyclopedia of Genes and Genomes) LIGAND database provides chemical structures for around 12 000 chemical compounds and drugs with biological information around 2000 compounds are annotated to enzymatic pathways. 

Figure 8.2. Query page for searching metabolic pathway between two compounds. A search for metabolic pathway(s) between two compounds in a specific organism can be performed at the KEGG server.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a data repository providing curated information on microbial catabolic enzymes and their organization into metabolic pathways 54. At present, the UM-BBD stores information on approximately 100 pathways with 700 reactions, 600 compounds and 400 enzymes. The database does not try to cover every known enzyme but rather focuses on those used for the biodegradation of xenobiotics. UM-BBD is linked to the ENZYME, BRENDA and KEGG/LIGAND databases mentioned above. 

KEGG, biosynthetic pathways Klotho of biochemical compounds Monosaccharide database ... 

Secondary metabolites are produced by plants in response to biotic or abiotic interactions with their environment and confer protection through a variety of antimicrobial, pesticidal, and pharmacological properties. Alkaloids are a class of plant secondary metabolites that traditionally have been classified as basic compounds derived firom amino acids that contain one or more heterocyclic nitrogen atom. About 20 % of plant species accumulate alkaloids, which are mostly derived from amino acids, e.g., phenylalanine, tyrosine, tryptophan, and lysine. The alkaloids are popular for their medicinal importance. The pharmaceutically important representatives of secondary metabolites are mostly alkaloids derived from tyrosine. In this chapter, we summarized the prior information, basic knowledge about the alkaloids, origin, physicochemical properties, uses, classification, biosynthetic reactions, and distribution of tyrosine-derived alkaloids especially opium alkaloids and their biosynthetic pathways in plants. We have also reviewed different web resources related to alkaloids and secondary metabolic pathway databases such as KEGG. 

The METLIN metabolite database is implemented using the open-source software tool, MySQL. Most compounds are annotated with both a chemical formula and structure. Individual metabolite is linked to outside resources such as the KEGG, Human Metabolome Database (HMDB), and the respective PubChem database entries through the included numbers of KEGG, HMDB, and Chemical Abstract Service (CAS), respectively. This kind of linkage makes it easy for the researchers to find further references and inquiries about the metabolite. 

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