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Prediction of compounds’ biological function (metabolic pathways) based on functional group composition

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Abstract

Efficient in silico screening approaches may provide valuable hints on biological functions of the compound-candidates, which could help to screen functional compounds either in basic researches on metabolic pathways or drug discovery. Here, we introduce a machine learning method (Nearest Neighbor Algorithm) based on functional group composition of compounds to the analysis of metabolic pathways. This method can quickly map small chemical molecules to the metabolic pathway that they likely belong to. A set of 2,764 compounds from 11 major classes of metabolic pathways were selected for study. The overall prediction rate reached 73.3%, indicating that functional group composition of compounds was really related to their biological metabolic functions.

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Authors and Affiliations

  1. CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China

    Yu-Dong Cai, Xin Meng & Guo-Dong Zhao

  2. Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester, M60 1QD, UK

    Yu-Dong Cai & Kai-Yan Feng

  3. Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100039, People’s Republic of China

    Ziliang Qian

  4. Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, People’s Republic of China

    Ziliang Qian

  5. Department of Biomedical Engineering, Shanghai Jiaotong University, Shanghai, 200240, People’s Republic of China

    Lin Lu

  6. School of Materials Science and Engineering, Shanghai University, 149 Yan-Chang Road, Shanghai, 200072, People’s Republic of China

    Bing Niu & Wen-Cong Lu

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  1. Yu-Dong Cai
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  2. Ziliang Qian
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  3. Lin Lu
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  4. Kai-Yan Feng
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  5. Xin Meng
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  6. Bing Niu
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  7. Guo-Dong Zhao
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  8. Wen-Cong Lu
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Corresponding author

Correspondence to Yu-Dong Cai.

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Cai, YD., Qian, Z., Lu, L. et al. Prediction of compounds’ biological function (metabolic pathways) based on functional group composition. Mol Divers 12, 131–137 (2008). https://doi.org/10.1007/s11030-008-9085-9

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  • DOI: https://doi.org/10.1007/s11030-008-9085-9

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