Metabolite and reaction inference based on enzyme specificities

Journal article (2009)
Faculty
Electrical Engineering, Mathematics and Computer Science (EEMCS) (TU Delft)
Copyright: M.J.L. de Groot, R.J.P. van Berlo, W.A. van Winden, P.J.T. Verheijen, M.J.T. Reinders and D. de Ridder. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License
DOI: https://doi.org/doi:10.1093/bioinformatics/btp507
OA-Fund TU Delft
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Published Date

20-08-2009

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Source:

Bioinformatics, Advance Access published on August 20, 2009

ISSN:

1460-2059

Faculty

Electrical Engineering, Mathematics and Computer Science

Abstract

Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this paper, we propose to model enzyme aspecificity by predicting whether an input compound is likely to be transformed by a certain enzyme. Such a predictor has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. Results: We have developed a system for metabolite and reaction inference based on enzyme specificities (MaRIboES). It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA. Leave-one-out cross-validation shows that 80% of known reactions are predicted well. Application to the yeast glycolytic and pentose phosphate pathways predicts a large number of known and new reactions, often leading to the formation of novel compounds, as well as a number of interesting bypasses and cross-links.

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