Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction

102Citations
Citations of this article
139Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Background: Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. Results: A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. Conclusion: NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites. © 2008 Kuhn et al; licensee BioMed Central Ltd.

Cite

CITATION STYLE

APA

Kuhn, S., Egert, B., Neumann, S., & Steinbeck, C. (2008). Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-400

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free