Automatic assignment of reaction operators to enzymatic reactions

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3135-3142

  Leber, Markus ^a   Egelhofer, Volker ^a,b   Schomburg, Ida ^a,b   Schomburg, Dietmar ^a,b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ARTICLE; BIOCATALYSIS; BIOLOGY; CHEMISTRY; CLASSIFICATION; ENZYME SPECIFICITY; KINETICS; METABOLISM; METHODOLOGY; PROTEIN DATABASE; THEORETICAL MODEL;

BIOCATALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYMES; KINETICS; MODELS, THEORETICAL; SUBSTRATE SPECIFICITY;

EID: 75949089439     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp549     Document Type: Article

References (22)

1. Apostolakis, J. et al. (2008) Automatic determination of reaction mappings and reaction center information. 2. Validation on a biochemical reaction database. J. Chem. Inform. Model., 48, 1190-1198.
2. Bauer, J. (1989) IGOR2: a PC-program for generating new reactions and molecular structures. Tetrahedron Comput. Methodol., 2, 269-280.
3. Brandt, J. and von Scholley, A. (1983) An efficient algorithm for the computation of the canonical numbering of reaction matrices. Comput. Chem., 7, 51-59.
4. Brandt, J. et al. (1981) Classification of reactions by electron shift patterns. Chemica Scripta., 18, 53-60.
5. Bron, C. and Kerbosch, J. (1973) Algorithm 457-finding all cliques of an undirected graph. Commun. ACM, 16, 575-577.
6. Dugundji, J. and Ugi, I. (1973) An algebraic model of constitutional chemistry as a basis for chemical computer programs. Topics Curr. Chem., 39, 19-64.
7. Fontain, E. and Reitsam, K. (1991) The generation of reaction networks with RAIN. 1. The reaction generator. J. Chem. Inform. Comp. Sci., 31, 96-101.
8. Hattori, M. et al. (2003) Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Amer. Chem. Soc., 125, 11853-11865.
9. Hatzimanikatis, V. et al. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics, 21, 1603-1609.
10. Koch, I. (2001) Enumerating all connected maximal common subgraphs in two graphs. Theoret. Comp. Sci., 250, 1-30.
11. Körner, R. and Apostolakis, J. (2008) Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach. J. Chem. Inform. Model., 48, 1181-1189.
12. Kotera, M. et al. (2004) Computational assignment of the EC-numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc., 126, 16487-16498.
13. Levi, G. (1972)Anote on the derivation of maximal common subgraphs of two directed or undirected graphs. Calcolo, 9, 341-352.
14. Marialke, J. et al. (2007) Graph-based molecular alignment (GMA). J. Chem. Inform. Model., 47, 591-601.
15. McGregor, J.J., (1982) Backtrack search algorithms and the maximal common subgraph problem. Software: Pract. Exp., 12, 23-34.
16. Oh, M. et al. (2007) Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model., 47, 1702-1712.
17. Raymond, J.W. and Willett, P. (2002) Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J. Comp.-Aid. Mol. Des., 16, 521-533.
18. Reitz, M. et al. (2004) Enabling the exploration of biochemical pathways. Org. Biomol. Chem., 2, 3226-3237.
19. Schomburg, I. et al. (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res., 32, D431-D433.
20. Tipton, K.F. and Boyce, S. (2000) History of the enzyme nomenclature system. Bioinformatics, 16, 34-40.
21. Ugi, I. et al. (1994) Models, concepts, theories, and formal languages in chemistry and their use as a basis for computer assictance in chemistry. J. Chem. Inform. Comp. Sci., 34, 3-16.
22. Webb, E.C. (1990) Enzyme Nomenclature-recommendations-1984-Supplement-3-corrections and additions. Eur. J. Biochem., 187, 263-281.