M-path: A compass for navigating potential metabolic pathways

Bioinformatics

Volumn 31, Issue 6, 2015, Pages 905-911

  Araki, Michihiro ^a   Cox, Robert Sidney ^a   Makiguchi, Hiroki ^b   Ogawa, Teppei ^b   Taniguchi, Takeshi ^c   Miyaoku, Kohei ^d   Nakatsui, Masahiko ^a   Hara, Kiyotaka Y ^a   Kondo, Akihiko ^a  

^a KOBE UNIVERSITY   (Japan)

^b Mitsui Knowledge Industry Co   (Japan)

^c MCHC RandD Synergy Center Inc   (Japan)

^d MITSUBISHI CHEMICAL CORPORATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ALGORITHM; COMPUTER PROGRAM; FACTUAL DATABASE; METABOLISM;

ALGORITHMS; AMINO ACIDS; DATABASES, FACTUAL; METABOLIC NETWORKS AND PATHWAYS; SOFTWARE;

EID: 84925264917     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu750     Document Type: Article

References (35)

1. Barabási, A.-L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
2. Bar-Even, A. and Salah Tawfik, D. (2013) Engineering specialized metabolic pathways-is there a room for enzyme improvements? Curr. Opin. Biotechnol., 24, 310-319.
3. Bar-Even, A. et al. (2011) The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry, 50, 4402-4410.
4. Carbonell, P. et al. (2012) Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst. Biol., 6, 10.
5. Carbonell, P. et al. (2014) XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. 42(Web Server issue):W389-W94.
6. Cho, A. et al. (2010) Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst. Biol., 4, 35.
7. Chou, C.-H. et al. (2009) FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res., 37, W129-W134.
8. Handorf, T. et al. (2005) Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol., 61, 498-512.
9. Hatzimanikatis, V. et al. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics, 21, 1603-1609.
10. Henry, C.S. et al. (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol. Bioeng, 106, 462-473.
11. Jankowski, M.D. et al. (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys. J., 95, 1487-1499.
12. Kanehisa, M. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
13. Keasling, J.D. (2010) Manufacturing molecules through metabolic engineering. Science, 330, 1355-1358.
14. Khersonsky, O. et al. (2011) Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions. Biochemistry, 50, 2683-2690.
15. Kumar, A. et al. (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics, 13, 6.
16. Lee, J.W. et al. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol., 8, 536-546.
17. Martin, C.H. et al. (2009) Synthetic metabolism: engineering biology at the protein and pathway scales. Chem. Biol., 16, 277-286.
18. McClymont, K. and Soyer, O.S. (2013) Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Res., 41, e113.
19. Medema, M.H. et al. (2012) Computational tools for the synthetic design of biochemical pathways. Nat. Rev. Microbiol., 10, 191-202.
20. Nakamura, M. et al. (2012) An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics, 13, S8.
21. NCBI Resource Coordinators (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 42(Database issue): D7-D17.
22. Nielsen, J. and Keasling, J.D. (2011) Synergies between synthetic biology and metabolic engineering. Nat. Biotechnol., 29, 693-695.
23. Nobeli, I. et al. (2009) Protein promiscuity and its implications for biotechnology. Nat. Biotechnol., 27, 157-167.
24. Noor, E. et al. (2010) Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol. Cell, 39, 809-820.
25. Orth, J.D. et al. (2010) What is flux balance analysis? Nat. Biotechnol., 28, 245-248.
26. Rahman, S.A. et al. (2014) EC-BLAST: a tool to automatically search and compare enzyme reactions. Nat. Methods, 11, 171-174.
27. Rocha, I. et al. (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol., 4, 45.
28. Rodrigo, G. et al. (2008) DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics, 24, 2554-2556.
29. Schomburg, I. et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res., 41, D764-D772.
30. Schulenburg, C. and Miller, B.G. (2014) Enzyme recruitment and its role in metabolic expansion. Biochemistry, 53, 836-845.
31. Soh, K.C. and Hatzimanikatis, V. (2010) DREAMS of metabolism. Trends Biotechnol. 28, 501-508.
32. Stephanopoulos, G. (2012) Synthetic biology and metabolic engineering. ACS Synth. Biol., 1, 514-525.
33. Willett, P. et al. (1998) Chemical similarity searching. J. Chem. Inf. Model., 38, 983-996.
34. Xia, D. et al. (2011) MRSD: a web server for metabolic route search and design. Bioinformatics, 27, 1581-1582.
35. Yim, H. et al. (2011) Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol. Nat. Chem. Biol., 7, 445-452.