Automatic assignment of EC numbers.

PLoS Computational Biology
Volker EgelhoferDietmar Schomburg

Abstract

A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology. When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function, the EC number introduced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) is used. However, each and every one of these applications is critically dependent upon the consistency and reliability of the underlying data for success. We have developed tools for the validation of the EC number classification scheme. In this paper, we present validated data of 3788 enzymatic reactions including 229 sub-subclasses of the EC classification system. Over 80% agreement was found between our assignment and the EC classification. For 61 (i.e., only 2.5%) reactions we found that their assignment was inconsistent with the rules of the nomenclature committee; they have to be transferred to other sub-subclasses. We demonstrate that our validation results can be used to initiate corrections and improvements to the EC number classification scheme.

References

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Citations

Jan 15, 2014·Nature Methods·Syed Asad RahmanJanet M Thornton
Feb 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Sergio Martínez CuestaJanet M Thornton
Jan 30, 2016·Journal of Chemical Information and Modeling·Yuki MoriyaSusumu Goto
Apr 15, 2011·Current Opinion in Chemical Biology·Daniel E Almonacid, Patricia C Babbitt
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Michiel StockWillem Waegeman
Aug 14, 2012·Current Opinion in Structural Biology·Nicholas FurnhamJanet M Thornton
Jul 19, 2015·Bioinformatics·Varun GiriAnirban Bhaduri
Apr 26, 2012·BMC Bioinformatics·Neetika Nath, John B O Mitchell
Apr 27, 2012·BMC Bioinformatics·Luna De FerrariIgor Goryanin
May 8, 2019·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Marilee Ann Benore
Jun 28, 2016·PLoS Computational Biology·Elisa Boari de LimaRaquel Cardoso de Melo-Minardi
Dec 8, 2016·Biophysics and Physicobiology·Masaaki Kotera, Susumu Goto
Feb 4, 2016·PloS One·Handan Melike DönertaşJanet M Thornton
Jul 5, 2018·BMC Bioinformatics·Tadi Venkata SivakumarTae Yong Kim
Nov 21, 2014·Journal of Chemical Information and Modeling·Akhil Kumar, Costas D Maranas

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Software Mentioned

SIMCOMP
Ensembl
BRENDA
MetaCyc

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