Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites

Bioinformatics

Volumn 22, Issue 24, 2006, Pages 3082-3088

  Mu, Fangping ^a   Unkefer, Pat J ^b   Unkefer, Clifford J ^b   Hlavacek, William S ^a,c  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b Bioscience Division   (United States)

^c CENTER FOR NONLINEAR STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL GROUP; GENE PRODUCT; OXIDOREDUCTASE;

ACCURACY; ARTICLE; BIOINFORMATICS; BIOTRANSFORMATION; CHEMICAL STRUCTURE; COMPUTER PROGRAM; ENZYME MECHANISM; ENZYME SUBSTRATE; GENE IDENTIFICATION; METABOLITE; METABOLOMICS; OXIDATION REDUCTION REACTION; PREDICTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; STRUCTURAL BIOINFORMATICS; SYSTEMS BIOLOGY;

EID: 33845365378     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl535     Document Type: Article

References (38)

1. Anari, M.R. and Baillie, T.A. (2005) Bridging chemoinformatic metabolite prediction and tandem mass spectrometry. Drug Discov. Today, 10, 711-717.
2. Breitling, R. et al. Precision mapping of the metabolome. Trends Biotechnol., doi:10.1016/j.tibtech.2006.10.006.
3. Chang, C.-C. and Lin,C.-J. (2001) LIBSVM: A library for support vector machines.
4. Colombo, G. and Carrea, G. (2002) Modeling enzyme reactivity in organic solvents and water through computer simulations. J. Biotechnol., 96, 23-33.
5. Cortes, C. and Vapnik, V. (1995) Support-vector networks. Mach. Learn., 20, 273-297.
6. Darvas, F. (1998) Predicting metabolic pathways by logic programming. J. Mol. Graphics, 6, 80-86.
7. Dunn, W.B. et al. (2005) Measuring the metabolome: Current analytical technologies. Analyst, 130, 606-625.
8. Fernie, A.R. et al. (2004) Metabolite profiling: From diagnostics to systems biology. Nat. Rev. Mol. Cell. Biol., 5, 763-769.
9. Fiehn, O. (2002) Metabolomics: The link between genotypes and phenotypes. Plant Mol. Biol., 48, 155-171.
10. Francke, C. et al. (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol., 13, 550-558.
11. Gasteiger, J. and Hutchings, M.G. (1984) Quantitative models of gas-phase protontransfer reactions involving alcohols, ethers, and their thio analoguess. Correlation analyses based on residual electronegativity and effective polarizability. J. Am. Chem. Soc., 106, 6489-6495.
12. Gasteiger, J. and Marsili, M. (1980) Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron, 36, 3219-3228.
13. Goodacre, R. et al. (2004) Metabolomics by numbers: Acquiring and understanding global metabolite data. Trends Biotechnol., 22, 245-252.
14. Goto, S. et al. (2002) LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30, 402-404.
15. Greene, N. et al. (1999) Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. SAR QSAR Environ. Res., 10, 299-313.
16. Hatzimanikafis, V. et al. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics, 21, 1603-1609.
17. Henkelman, G. et al. (2005) Conformational dependence of a protein kinase phosphate transfer reaction. Proc. Natl Acad. Sci. USA, 102, 15347-15351.
18. Hou, B.K. et al. (2003) Microbial pathway prediction: A functional group approach. J. Chem. Inf. Comput. Sci., 43, 1051-1057.
19. Hutchings, M.G. and Gasteiger, J. (1983) Residual electronegativity - an empirical quantification of polar influences and its application to the proton affinity of amines. Tetrahedron Lett., 24, 2541-2544.
20. James, C.A. et al. (2005) Daylight Theory Manual, version 4.9, Ch. 4. Daylight Chemical Information Systems, Inc., Aliso Viejo, CA.
21. Jaworska, J. et al. (2002) Probabilistic assessment of biodegradability based on meta-bolic pathways: CATBOL System. SAR QSAR Environ. Res., 13, 307-323.
22. Karelson, M. et al. (1996) Quantum-chemical descriptors in QSAR/QSPR studies. Chem. Rev., 96, 1027-1043.
23. Kell, D.B. (2004) Metabolomics and systems biology: Making sense of the soup. Curr. Opin. Microbiol., 7, 296-307.
24. Klopman, G. et al. (1994) META. 1. A program for the evaluation of metabolic transformation of chemicals. J. Chem. Inf. Comput. Sci., 34, 1320-1325.
25. Langowski, J. and Long, A. (2002) Computer systems for the prediction of xenobiotic metabolism. Adv. Drug Deliv. Rev. 54, 407-415.
26. Mayeno, A.N. et al. (2005) Biochemical reaction network modeling: predicting metabolism of organic chemical mixtures. Environ. Sci. Technol., 39, 5363-5371.
27. McShan, D.C. et al. (2004) Symbolic inference of xenobiotic metabolism. Pac. Symp. Biocomput., 9, 545-546.
28. Payne, M.P. (2004) Computer-based methods for the prediction of chemical metabolism and biotransformation within biological organisms. In Cronin, M.T.D. and Livingstone, D.J. (eds), Predicting Chemical Toxicity and Fate. CRC Press, Boca Raton, pp. 205-227.
29. Schloss, P.D. and Handelsman, J. (2005) Metagenomics for studying unculturable microorganisms: Cutting the Gordian knot. Genome Biol., 6, 229.
30. Silverman, R.B. (2000) The Organic Chemistry of Enzyme-Catalyzed Reactions. Academic Press, San Diego, CA.
31. Steinbeck, C. et al. (2003) The Chemistry Development Kit(CDK): An open-source Java library for chemo-and bioinformatics. J. Chem. Inf. Comput. Sci., 43, 493-500.
32. Talafous, J. et al. (1994) META. 2. A dictionary model of mammalian xenobiotic metabolism. J. Chem. Inf. Comput. Sci., 34, 1326-1333.
33. Vapnik, V.N. (1998) Statistical Learning Theory. Wiley, NY.
34. Wagner, C. et al. (2003) Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry, 62, 887-900.
35. Wall, M.E. et al. (2004) Design of gene circuits: Lessons from bacteria. Nat. Rev. Genet., 5, 34-42.
36. Walters, W.P. and Yalkowsky, S.H. (1996) ESCHER - a computer program for the determination of external rotational symmetry numbers from molecular topology. J. Chem. Inf. Comput. Sci., 36, 1015-1017.
37. Wegner, J.K. (2004) JOELib Tutorial: A Java based cheminformatics/ computational chemistry package.
38. Wegner, J.K. and Zell, A. (2003) Prediction of aqueous solubility and partition coefficient optimized by a genetic algorithm based descriptor selection method. J. Chem. Inf. Comput. Sci, 43, 1077-1084.