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Similar articles for PubMed (Select 17516640)

1.

Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways.

Oh M, Yamada T, Hattori M, Goto S, Kanehisa M.

J Chem Inf Model. 2007 Jul-Aug;47(4):1702-12. Epub 2007 May 22.

PMID:
17516640
2.

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments.

Yamanishi Y, Tabei Y, Kotera M.

Bioinformatics. 2015 Jun 15;31(12):i161-i170. doi: 10.1093/bioinformatics/btv224.

3.

Chemical reactivity drives spatiotemporal organisation of bacterial metabolism.

de Lorenzo V, Sekowska A, Danchin A.

FEMS Microbiol Rev. 2015 Jan;39(1):96-119. doi: 10.1111/1574-6976.12089. Epub 2014 Dec 4. Review.

PMID:
25227915
4.

Emerging chemicals and the evolution of biodegradation capacities and pathways in bacteria.

Kolvenbach BA, Helbling DE, Kohler HP, Corvini PF.

Curr Opin Biotechnol. 2014 Jun;27:8-14. doi: 10.1016/j.copbio.2013.08.017. Epub 2013 Sep 17. Review.

PMID:
24863891
5.

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics.

Kotera M, Tabei Y, Yamanishi Y, Moriya Y, Tokimatsu T, Kanehisa M, Goto S.

BMC Syst Biol. 2013;7 Suppl 6:S2. doi: 10.1186/1752-0509-7-S6-S2. Epub 2013 Dec 13.

6.

Enzyme reaction annotation using cloud techniques.

Huang CC, Lin CY, Chang CW, Tang CY.

Biomed Res Int. 2013;2013:140237. doi: 10.1155/2013/140237. Epub 2013 Sep 26.

7.

Elucidation of metabolic pathways from enzyme classification data.

McDonald AG, Tipton KF.

Methods Mol Biol. 2014;1083:173-86. doi: 10.1007/978-1-62703-661-0_11.

PMID:
24218216
8.

Origins of activity enhancement in enzyme cascades on scaffolds.

Idan O, Hess H.

ACS Nano. 2013 Oct 22;7(10):8658-65. doi: 10.1021/nn402823k. Epub 2013 Sep 9.

PMID:
24007359
9.

Chemical and genomic evolution of enzyme-catalyzed reaction networks.

Kanehisa M.

FEBS Lett. 2013 Sep 2;587(17):2731-7. doi: 10.1016/j.febslet.2013.06.026. Epub 2013 Jun 28. Review.

10.

Modular architecture of metabolic pathways revealed by conserved sequences of reactions.

Muto A, Kotera M, Tokimatsu T, Nakagawa Z, Goto S, Kanehisa M.

J Chem Inf Model. 2013 Mar 25;53(3):613-22. doi: 10.1021/ci3005379. Epub 2013 Feb 19.

11.

Relationship between extreme pathways and structurally minimal pathways.

Barany M, Bertok B, Fan LT, Friedler F.

Bioprocess Biosyst Eng. 2013 Sep;36(9):1199-203. doi: 10.1007/s00449-012-0847-5. Epub 2012 Nov 10.

PMID:
23142845
12.

Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation.

Ellis LB, Wackett LP.

Microb Inform Exp. 2012 Jan 4;2(1):1. doi: 10.1186/2042-5783-2-1.

13.

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.

Mu F, Unkefer CJ, Unkefer PJ, Hlavacek WS.

Bioinformatics. 2011 Jun 1;27(11):1537-45. doi: 10.1093/bioinformatics/btr177. Epub 2011 Apr 8.

14.

A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms.

Andreini C, Bertini I, Cavallaro G, Decaria L, Rosato A.

J Chem Inf Model. 2011 Mar 28;51(3):730-8. doi: 10.1021/ci100392q. Epub 2011 Mar 10.

PMID:
21388232
15.

Structure-based interpretation of biotransformation pathways of amide-containing compounds in sludge-seeded bioreactors.

Helbling DE, Hollender J, Kohler HP, Fenner K.

Environ Sci Technol. 2010 Sep 1;44(17):6628-35. doi: 10.1021/es101035b.

PMID:
20690778
16.

Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition.

Chen L, Feng KY, Cai YD, Chou KC, Li HP.

BMC Bioinformatics. 2010 May 31;11:293. doi: 10.1186/1471-2105-11-293.

17.

PathPred: an enzyme-catalyzed metabolic pathway prediction server.

Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W138-43. doi: 10.1093/nar/gkq318. Epub 2010 Apr 30.

18.
19.

Computational framework for predictive biodegradation.

Finley SD, Broadbelt LJ, Hatzimanikatis V.

Biotechnol Bioeng. 2009 Dec 15;104(6):1086-97. doi: 10.1002/bit.22489.

20.

Systematic extraction of structure-activity relationship information from biological screening data.

Wawer M, Bajorath J.

ChemMedChem. 2009 Sep;4(9):1431-8. doi: 10.1002/cmdc.200900222.

PMID:
19621333
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