Abstract
Protein–protein interaction plays a fundamental role in many biological processes and diseases. Characterizing protein interaction sites is crucial for the understanding of the mechanism of protein–protein interaction and their cellular functions. In this paper, we proposed a method based on integrated support vector machine (SVM) with a hybrid kernel to predict protein interaction sites. First, a number of features of the protein interaction sites were extracted. Secondly, the technique of sliding window was used to construct a protein feature space based on the influence of the adjacent residues. Thirdly, to avoid the impact of imbalance of the data set on prediction accuracy, we employed boost-strap to re-sample the data. Finally, we built a SVM classifier, whose hybrid kernel comprised a Gaussian kernel and a Polynomial kernel. In addition, an improved particle swarm optimization (PSO) algorithm was applied to optimize the SVM parameters. Experimental results show that the PSO-optimized SVM classifier outperforms existing methods.
Similar content being viewed by others
References
Alberts BD, Bray D, Lewis J et al (1989) Molecular biology of the cell. Garland, New York
Ni QS, Wang ZZ, Wang GY et al (2008) Prediction of protein–protein interactions based on local support vector machine. J Biomed Eng Res 02(9):1106–1109
Yan CH, Dobbs D, Honavar V et al (2004) A two stage classifier for identification of protein–protein interface residues. Bioinformatics 20(1):371–378
Chen XW, Jeong JC (2009) Sequence-based prediction of protein interaction sites with an integrative method. Bioinformatics 25(5):585–591
Chen YH, Xu JR, Bin Yang et al (2012) A novel method for prediction of protein interaction sites based on integrated RBF neural networks. Comput Biol Med 42:402–407
Meng W, Wang F, Peng X (2008) Prediction of protein–protein interaction sites using support vector machine. Appl Sci 26(4):403–408
Minakuehi Y, Satou K, Konagaya A (2002) Prediction of protein–protein interaction sites using support vector machines. Genome Inform 13:322–323
LiQin Jin (2007) Biological chemistry. Zhejiang University Press, Hangzhou (in Chinese)
Marangoni F, Barberis M, Botta M (2003) Large scale prediction of protein interactions by a SVM-based method. In: Neural Nets, vol 2859. Springer, Berlin Heidelberg, pp 296–301
Li Liu (2009) The research and validation of support vector machine (SVM) algorithm with different kernels. Jiangnan University, Wuxi, Jiangsu (in Chinese)
Cortes C, Vapnik V (1995) Support vector network. Mach, Learn
Chatterjee P, Basu S, Kundu M et al (2011) PPI_SVM: prediction of protein–protein interactions using machine learning domain–domain affinities and frequency tables. Cell Mol Biol Lett 16:264–278
Aimin Zhou, Bo-Yang Qub, Hui Li et al (2011) Multiobjective evolutionary algorithms: a survey of the state of the art. Swarm Evol Comput 1(1):32–49
Xing X, Chen Y, Yang B (2010) Dimensional reduction based on conservative adaptive K-nearest neighbor algorithm. Univ Jinan Sci Technol 2:159–162 (in Chinese)
Acknowledgments
This work was funded by the Natural Science Foundation of Fujian Province (2012J05114, 2013N5006), Special Project on the Integration of Industry, Fuzhou City Science Foundation (2012G106). We also want to thank for the help from Dr. Zhibin Fu.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Guo, H., Liu, B., Cai, D. et al. Predicting protein–protein interaction sites using modified support vector machine. Int. J. Mach. Learn. & Cyber. 9, 393–398 (2018). https://doi.org/10.1007/s13042-015-0450-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13042-015-0450-6