title: SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.
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.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hattori
authors.forename: Nobuya
authors.initials: N
authors.lastname: Tanaka
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
mesh_terms: D003196:Computer Graphics; D016208:Databases, Factual; D020407:Internet; D007536:Isomerism; D053858:Metabolic Networks and Pathways; D015394:Molecular Structure; D012984:Software; D014584:User-Computer Interface
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33
references.pmid: 19498078
references.citation: J Chem Inf Comput Sci. 2002 Nov-Dec;42(6):1296-310
references.pmid: 12444726
references.citation: J Chem Inf Model. 2009 Jan;49(1):22-7
references.pmid: 19072559
references.citation: Pharmacogenomics. 2001 Nov;2(4):373-85
references.pmid: 11722287
references.citation: J Am Chem Soc. 2003 Oct 1;125(39):11853-65
references.pmid: 14505407
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
references.pmid: 18077471
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):402-4
references.pmid: 11752349
references.citation: Nat Chem Biol. 2007 Aug;3(8):447-50
references.pmid: 17637771
references.citation: Biomol Eng. 2007 Sep;24(3):327-35
references.pmid: 17433774
references.citation: Genome Inform. 2003;14:144-53
references.pmid: 15706529