SIMCOMP/SUBCOMP: Chemical structure search servers for network analyses

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Hattori, Masahiro ^a   Tanaka, Nobuya ^a,b   Kanehisa, Minoru ^a   Goto, Susumu ^a  

^a KYOTO UNIVERSITY   (Japan)

^b FUJIFILM CORPORATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CHEMICAL STRUCTURE; CHIRALITY; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA BASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; PRIORITY JOURNAL; VALIDITY; WEB BROWSER; COMPUTER GRAPHICS; COMPUTER INTERFACE; FACTUAL DATABASE; INTERNET; ISOMERISM; METABOLISM;

COMPUTER GRAPHICS; DATABASES, FACTUAL; INTERNET; ISOMERISM; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR STRUCTURE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77954288984     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq367     Document Type: Article

References (17)

1. Kanehisa, M. (2001) Prediction of higher order functional networks from genomic data. Pharmacogenomics, 2, 373-385.
2. Oprea, T.I., Tropsha, A., Faulon, J.L. and Rintoul, M.D. (2007) Systems chemical biology. Nat. Chem. Biol., 8, 447-450.
3. Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J. and Bryant, S.H. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 37, W623-W633.
4. Hattori, M., Okuno, Y., Goto, S. and Kanehisa, M. (2003) Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc., 125, 11853-11865.
5. Hattori, M., Okuno, Y., Goto, S. and Kanehisa, M. (2003) Heuristics for chemical compound matching. Genome Inform., 14, 144-153.
6. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
7. Dalby, A., Nourse, J.G., Hounshell, W.D., Gushurst, A.K.I., Grier, D.L., Leland, B.A. and Laufer, J. (1992) Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J. Chem. Inf. Comput. Sci., 32, 244-255.
8. Weininger, D. (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci., 28, 31-36.
9. Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30, 402-404.
10. Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M., Asahi, H., Kurokawa, K., Arita, M., Saito, K., Ohta, D., Shibata, D. and Kanaya, S. (2006) KNApSAcK: A comprehensive species-metabolite relationship database. Biotechnol. Agric. For., 57, 165-181.
11. Willett, P., Barnard, J. and Downs, G.M. (1998) Chemical similarity searching. J. Chem. Inf. Comput. Sci., 38, 983-996.
12. Ullmann, J.R. (1976) An algorithm for subgraph isomorphism. J. ACM, 23, 31-42.
13. Golovin, A. and Henrick, K. (2009) Chemical substructure search in SQL. J. Chem. Inf. Model., 49, 22-27.
14. Chen, L., Nourse, J.G., Christie, B.D., Leland, B.A. and Grier, D.L. (2002) Over 20 years of reaction access systems from MDL: a novel reaction substructure search algorithm. J. Chem. Inf. Comput. Sci., 42, 1296-1310.
15. Berks, A.H. (2003) Current state of the art of Markush topological search systems. In Gasteiger, J. (ed.), Handbook of Chemoinformatics: from Data to Knowledge, Vol. 2. Wiley-VCH, Weinheim, pp. 885-903.
16. Liliana, F. and Valiente, G. (2007) Validation of metabolic pathway databases based on chemical substructure search. Biomol. Eng., 24, 327-335.
17. Cordella, L.P., Foggia, P., Sansone, C. and Vento, M. (1996) An efficient algorithm for the inexact matching of ARG using a contextual transformational model. Proceedings of the 13th ICPR, Vol. III. IEEE Computer Society Press, Washington, DC, pp. 180-184.