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Prediction of interaction between small molecule and enzyme using AdaBoost

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Abstract

The knowledge of whether one enzyme can interact with a small molecule is essential for understanding the molecular and cellular functions of organisms. In this paper, we introduce a classifier to predict the small molecule– enzyme interaction, i.e., whether they can interact with each other. Small molecules are represented by their chemical functional groups, and enzymes are represented by their biochemical and physicochemical properties, resulting in a total of 160 features. These features are input into the AdaBoost classifier, which is known to have good generalization ability to predict interaction. As a result, the overall prediction accuracy, tested by tenfold cross-validation and independent sets, is 81.76% and 83.35%, respectively, suggesting that this strategy is effective. In this research, we typically choose interactions between small molecules and enzymes involved in metabolism to ultimately improve further understanding of metabolic pathways. An online predictor developed by this research is available at http://chemdata.shu.edu.cn/small_m.

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Authors and Affiliations

  1. Shanghai University, 149 Yan-Chang Road, Shanghai, 200072, China

    Bing Niu

  2. Department of Chemistry, College of Sciences, Shanghai University, 99 Shang-Da Road, Shanghai, 200444, China

    Yuhuan Jin & Wencong Lu

  3. Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200040, China

    Lin Lu

  4. Division of Imaging Science & Biomedical Engineering, The University of Manchester, Room G424, Stopford Building, Manchester, M13 9PT, UK

    Kaiyan Fen

  5. Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China

    Lei Gu & Yixue Li

  6. Department of Bioinformatics, College of Life Sciences, Zhejiang University, HangZhou, ZheJiang, 310058, China

    Zhisong He

  7. Shanghai Center for Bioinformation Technology, Shanghai, 200235, China

    Yixue Li

  8. College of Life Science& Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Yixue Li

  9. Institute of System Biology, Shanghai University, 99 ShangDa Road, Shanghai, 200244, China

    Yudong Cai

  10. Department of Combinatorics and Geometry, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Yudong Cai

Authors
  1. Bing Niu
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  2. Yuhuan Jin
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  3. Lin Lu
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  4. Kaiyan Fen
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  5. Lei Gu
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  6. Zhisong He
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  7. Wencong Lu
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  8. Yixue Li
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  9. Yudong Cai
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Corresponding authors

Correspondence to Wencong Lu or Yudong Cai.

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Niu, B., Jin, Y., Lu, L. et al. Prediction of interaction between small molecule and enzyme using AdaBoost. Mol Divers 13, 313–320 (2009). https://doi.org/10.1007/s11030-009-9116-1

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  • DOI: https://doi.org/10.1007/s11030-009-9116-1

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