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Predicting the distance between antibody’s interface residue and antigen to recognize antigen types by support vector machine

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Abstract

In this paper, a machine learning approach, known as support vector machine (SVM) is employed to predict the distance between antibody’s interface residue and antigen in antigen–antibody complex. The heavy chains, light chains and the corresponding antigens of 37 antibodies are extracted from the antibody–antigen complexes in protein data bank. According to different distance ranges, sequence patch sizes and antigen classes, a number of computational experiments are conducted to describe the distance between antibody’s interface residue and antigen with antibody sequence information. The high prediction accuracy of both self-consistent and cross-validation tests indicates that the sequential discovered information from antibody structure characterizes much in predicting the distance between antibody’s interface residue and antigen. Furthermore, the antigen class is predicted from residue composition information that belongs to different distance range by SVM, which shows some potential significance.

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Acknowledgments

This research has been partially supported by a 973 Project grant (2004CB720103) from the Ministry of Science and Technology, China and the grants (70531040, 70472074) from the National Natural Science Foundation, China. We would like to express our thanks to Mrs. Li Zhang, Northeastern University, USA and Mr. Gang Kou, University of Nebraska, USA for their constructive comments.

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Authors and Affiliations

  1. Research Center on Data Technology and Knowledge Economy, Graduate University of Chinese Academy of Sciences, Beijing, 100080, China

    Yong Shi, Xinyang Zhang & Wei Yin

  2. Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China

    Jia Wan

  3. Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka, 574-8530, Japan

    Yong Wang

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

    Zhiwei Cao

  5. Shanghai International Cancer Institute of China, Shanghai, 200433, China

    Yajun Guo

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  1. Yong Shi
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  2. Xinyang Zhang
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  3. Jia Wan
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  4. Yong Wang
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  5. Wei Yin
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  6. Zhiwei Cao
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Correspondence to Yong Shi.

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Shi, Y., Zhang, X., Wan, J. et al. Predicting the distance between antibody’s interface residue and antigen to recognize antigen types by support vector machine. Neural Comput & Applic 16, 481–490 (2007). https://doi.org/10.1007/s00521-006-0076-4

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  • DOI: https://doi.org/10.1007/s00521-006-0076-4

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