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Nucleic Acids Res. 2010 Jul;38(Web Server issue):W652-6. doi: 10.1093/nar/gkq367. Epub 2010 May 11.

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.

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  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Abstract

One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways. Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www.genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome.jp/tools/subcomp/) for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases. The SIMCOMP is a graph-based method for searching the maximal common subgraph isomorphism by finding the maximal cliques in the association graph. In contrast, the SUBCOMP is an extended method for solving the subgraph isomorphism problem. The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks.

PMID:
20460463
[PubMed - indexed for MEDLINE]
PMCID:
PMC2896122
Free PMC Article

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