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Prediction of protein structure class by coupling improved genetic algorithm and support vector machine

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Abstract

Structural class characterizes the overall folding type of a protein or its domain. Most of the existing methods for determining the structural class of a protein are based on a group of features that only possesses a kind of discriminative information for the prediction of protein structure class. However, different types of discriminative information associated with primary sequence have been completely missed, which undoubtedly has reduced the success rate of prediction. We present a novel method for the prediction of protein structure class by coupling the improved genetic algorithm (GA) with the support vector machine (SVM). This improved GA was applied to the selection of an optimized feature subset and the optimization of SVM parameters. Jackknife tests on the working datasets indicated that the prediction accuracies for the different classes were in the range of 97.8–100% with an overall accuracy of 99.5%. The results indicate that the approach has a high potential to become a useful tool in bioinformatics.

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Acknowledgments

The authors acknowledge financial support from the National Natural Science Foundation of China (Nos. 20475068, 20575082), the Natural Science Foundation of Guangdong Province (No. 031577, 7003714), the Scientific Technology Project of Guangdong Province (No. 2005B30101003) and the Scientific Technology Project of Guangzhou City (No. 2007Z3-E0441).

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  1. School of Chemistry and Chemical Engineering, Sun Yat-Sen University, 510275, Guangzhou, People’s Republic of China

    Z.-C. Li, X.-B. Zhou, Y.-R. Lin & X.-Y. Zou

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Li, ZC., Zhou, XB., Lin, YR. et al. Prediction of protein structure class by coupling improved genetic algorithm and support vector machine. Amino Acids 35, 581–590 (2008). https://doi.org/10.1007/s00726-008-0084-z

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  • DOI: https://doi.org/10.1007/s00726-008-0084-z

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