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Automatic assignment of EC numbers.

Egelhofer V, Schomburg I, Schomburg D - PLoS Comput. Biol. (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biochemistry, Technical University Braunschweig, Braunschweig, Germany. volker.egelhofer@univie.ac.at

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.

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Examples for the different subsets.(a) The reverse direction of the reaction is shown. (b) Ambiguous, fits more than one sub-subclass. (c) Reaction is assigned to a wrong sub-subclass. (d) The enzyme catalysis two or more different types of reaction, where at least one does not meet the requirements of the assigned sub-subclass.
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pcbi-1000661-g002: Examples for the different subsets.(a) The reverse direction of the reaction is shown. (b) Ambiguous, fits more than one sub-subclass. (c) Reaction is assigned to a wrong sub-subclass. (d) The enzyme catalysis two or more different types of reaction, where at least one does not meet the requirements of the assigned sub-subclass.

Mentions: As shown in Table 1, subset 2 covers all reactions in the EC system where instead of the correct – the reverse direction of reaction is shown. For example the reaction catalysed by arsenate reductase (EC 1.20.4.1, see Figure 2a) assigned to the sub-subclass 1.20.4 which covers enzymes ‘Acting on phosphorus or arsenic in donors, with a disulfide as acceptor’ as defined by the NC-IUBMB.


Automatic assignment of EC numbers.

Egelhofer V, Schomburg I, Schomburg D - PLoS Comput. Biol. (2010)

Examples for the different subsets.(a) The reverse direction of the reaction is shown. (b) Ambiguous, fits more than one sub-subclass. (c) Reaction is assigned to a wrong sub-subclass. (d) The enzyme catalysis two or more different types of reaction, where at least one does not meet the requirements of the assigned sub-subclass.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2813261&req=5

pcbi-1000661-g002: Examples for the different subsets.(a) The reverse direction of the reaction is shown. (b) Ambiguous, fits more than one sub-subclass. (c) Reaction is assigned to a wrong sub-subclass. (d) The enzyme catalysis two or more different types of reaction, where at least one does not meet the requirements of the assigned sub-subclass.
Mentions: As shown in Table 1, subset 2 covers all reactions in the EC system where instead of the correct – the reverse direction of reaction is shown. For example the reaction catalysed by arsenate reductase (EC 1.20.4.1, see Figure 2a) assigned to the sub-subclass 1.20.4 which covers enzymes ‘Acting on phosphorus or arsenic in donors, with a disulfide as acceptor’ as defined by the NC-IUBMB.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biochemistry, Technical University Braunschweig, Braunschweig, Germany. volker.egelhofer@univie.ac.at

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.

Show MeSH
Related in: MedlinePlus