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Identification of DNA-Binding Proteins via Fuzzy Multiple Kernel Model and Sequence Information

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Intelligent Computing Theories and Application (ICIC 2019)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11644))

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Abstract

DNA-binding proteins is the molecular basis for understanding the basic processes of life activities. Many diseases are associated with DNA binding proteins. The methods of detecting DNA-binding proteins are mainly realized by biochemical experiment, which is time consuming and extremely expensive. A lot of computational methods based on Machine Learning (ML) algorithm have been developed to detect DNA-binding proteins. In this study, we propose a novel DNA-binding proteins model via a Fuzzy Multiple Kernel Support Vector Machine. The multiple features of sequence and evolutionary are extracted and constructed as multiple kernels, respectively. Next, these corresponding kernels are integrated by Multiple Kernel Learning (MKL) algorithm. At last, Fuzzy Support Vector Machine (FSVM) is employed to build an effective DNA-binding protein predictor. Comparing with other outstanding methods, our proposed approach achieves good results. The accuracy of our model are 82.98% and 81.70% on PDB1075 (benchmark data set of DNA-binding proteins) and PDB186 (independent test set), respectively. Our approach is comparable to previous methods.

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Acknowledgments

This work is supported by a grant from the National Science Foundation of China (NSFC 61772362).

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Authors and Affiliations

  1. School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, People’s Republic of China

    Yijie Ding

  2. School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, No. 135, Yaguan Road, Tianjin Haihe Education Park, Tianjin, People’s Republic of China

    Jijun Tang & Fei Guo

  3. Department of Computer Science and Engineering, University of South Carolina, Columbia, USA

    Jijun Tang

Authors
  1. Yijie Ding
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  2. Jijun Tang
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  3. Fei Guo
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Corresponding author

Correspondence to Fei Guo .

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Editors and Affiliations

  1. Tongji University, Shanghai, China

    De-Shuang Huang

  2. University of Ulsan, Ulsan, Korea (Republic of)

    Kang-Hyun Jo

  3. Nanchang Institute of Technology, Nanchang, China

    Zhi-Kai Huang

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Ding, Y., Tang, J., Guo, F. (2019). Identification of DNA-Binding Proteins via Fuzzy Multiple Kernel Model and Sequence Information. In: Huang, DS., Jo, KH., Huang, ZK. (eds) Intelligent Computing Theories and Application. ICIC 2019. Lecture Notes in Computer Science(), vol 11644. Springer, Cham. https://doi.org/10.1007/978-3-030-26969-2_45

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  • DOI: https://doi.org/10.1007/978-3-030-26969-2_45

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-26968-5

  • Online ISBN: 978-3-030-26969-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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