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Items: 1 to 20 of 99

1.

Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints.

Hu QN, Zhu H, Li X, Zhang M, Deng Z, Yang X, Deng Z.

PLoS One. 2012;7(12):e52901. doi: 10.1371/journal.pone.0052901. Epub 2012 Dec 28.

2.

Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.

Kotera M, Okuno Y, Hattori M, Goto S, Kanehisa M.

J Am Chem Soc. 2004 Dec 22;126(50):16487-98.

PMID:
15600352
3.

Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps.

Latino DA, Zhang QY, Aires-de-Sousa J.

Bioinformatics. 2008 Oct 1;24(19):2236-44. doi: 10.1093/bioinformatics/btn405. Epub 2008 Aug 1.

PMID:
18676416
4.

Assignment of EC numbers to enzymatic reactions with MOLMAP reaction descriptors and random forests.

Latino DA, Aires-de-Sousa J.

J Chem Inf Model. 2009 Jul;49(7):1839-46. doi: 10.1021/ci900104b.

PMID:
19588957
5.

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism.

Saigo H, Hattori M, Kashima H, Tsuda K.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S31. doi: 10.1186/1471-2105-11-S1-S31.

6.

ECOH: an enzyme commission number predictor using mutual information and a support vector machine.

Matsuta Y, Ito M, Tohsato Y.

Bioinformatics. 2013 Feb 1;29(3):365-72. doi: 10.1093/bioinformatics/bts700. Epub 2012 Dec 5.

PMID:
23220570
7.

Generalized reaction patterns for prediction of unknown enzymatic reactions.

Shimizu Y, Hattori M, Goto S, Kanehisa M.

Genome Inform. 2008;20:149-58.

PMID:
19425130
8.

Automatic assignment of reaction operators to enzymatic reactions.

Leber M, Egelhofer V, Schomburg I, Schomburg D.

Bioinformatics. 2009 Dec 1;25(23):3135-42. doi: 10.1093/bioinformatics/btp549. Epub 2009 Sep 25.

PMID:
19783831
9.

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.

Yamanishi Y, Hattori M, Kotera M, Goto S, Kanehisa M.

Bioinformatics. 2009 Jun 15;25(12):i179-86. doi: 10.1093/bioinformatics/btp223.

10.

Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000700. doi: 10.1371/journal.pcbi.1000700.

11.

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

Green ML, Karp PD.

Nucleic Acids Res. 2005 Jul 20;33(13):4035-9. Print 2005.

12.

EC-BLAST: a tool to automatically search and compare enzyme reactions.

Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.

Nat Methods. 2014 Feb;11(2):171-4. doi: 10.1038/nmeth.2803. Epub 2014 Jan 12.

13.

Classification of chemical reactions and chemoinformatic processing of enzymatic transformations.

Latino DA, Aires-de-Sousa J.

Methods Mol Biol. 2011;672:325-40. doi: 10.1007/978-1-60761-839-3_13.

PMID:
20838975
14.

Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity.

Schneider N, Lowe DM, Sayle RA, Landrum GA.

J Chem Inf Model. 2015 Jan 26;55(1):39-53. doi: 10.1021/ci5006614. Epub 2015 Jan 13. Erratum in: J Chem Inf Model. 2015 Feb 23;55(2):474.

PMID:
25541888
15.

Automatic assignment of EC numbers.

Egelhofer V, Schomburg I, Schomburg D.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000661. doi: 10.1371/journal.pcbi.1000661.

16.

LIGAND database for enzymes, compounds and reactions.

Goto S, Nishioka T, Kanehisa M.

Nucleic Acids Res. 1999 Jan 1;27(1):377-9.

17.

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S.

J Chem Inf Model. 2016 Mar 28;56(3):510-6. doi: 10.1021/acs.jcim.5b00216. Epub 2016 Feb 17.

PMID:
26822930
18.

Semisupervised Gaussian Process for Automated Enzyme Search.

Mellor J, Grigoras I, Carbonell P, Faulon JL.

ACS Synth Biol. 2016 Jun 17;5(6):518-28. doi: 10.1021/acssynbio.5b00294. Epub 2016 Mar 30.

PMID:
27007080
19.

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function.

Žváček C, Friedrichs G, Heizinger L, Merkl R.

BMC Bioinformatics. 2015 Nov 4;16:359. doi: 10.1186/s12859-015-0807-6.

20.

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