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Protein & Peptide Letters


ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Predicting the Metabolic Pathways of Small Molecules Based on Their Physicochemical Properties

Author(s): Chun-Rong Peng, Wen-Cong Lu, Bing Niu, Min-Jie Li, Xiao-YanYang and Mi-Lin Wu

Volume 19 , Issue 12 , 2012

Page: [1250 - 1256] Pages: 7

DOI: 10.2174/092986612803521585


How to correctly and efficiently map small molecule to its possible metabolic pathway is a meaningful topic to metabonomics research. In this work, a novel approach to address this problem was introduced to encode physicochemical properties of small molecules. Based on this encoding method, a two stage feature selection method called mRMR-FFSAdaBoost was adopted to map small molecules to their corresponding metabolic pathways possible. As a result, the accuracies of 10-folds cross-validation test and independent set test for predicting the metabolic pathways of small molecules reached 83.88% and 85.23%, respectively. An online server for predicting metabolic pathways of unknown small molecules as described in this paper is accessible at

Keywords: ChemAxon, jchem for excel, KEGG, metabolic pathway, online server, small molecules, web-server, biochemical reactions, living systems, biological functions.

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