Prediction of the β-Hairpins in Proteins Using Support Vector Machine

被引：0
|
作者：
Xiu Zhen Hu
Qian Zhong Li
机构：
[1] Inner Mongolia University,Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology
[2] Inner Mongolia University of Technology,Department of Physics, College of Sciences
来源：
The Protein Journal | 2008年 / 27卷
关键词：
β-Hairpin motif; Supersecondary structure; Scoring function; Increment of diversity; Support vector machine;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
By using of the composite vector with increment of diversity and scoring function to express the information of sequence, a support vector machine (SVM) algorithm for predicting β-hairpin motifs is proposed. The prediction is done on a dataset of 3,088 non homologous proteins containing 6,027 β-hairpins. The overall accuracy of prediction and Matthew’s correlation coefficient are 79.9% and 0.59 for the independent testing dataset. In addition, a higher accuracy of 83.3% and Matthew’s correlation coefficient of 0.67 in the independent testing dataset are obtained on a dataset previously used by Kumar et al. (Nuclic Acid Res 33:154–159). The performance of the method is also evaluated by predicting the β-hairpins of in the CASP6 proteins, and the better results are obtained. Moreover, this method is used to predict four kinds of supersecondary structures. The overall accuracy of prediction is 64.5% for the independent testing dataset.
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页码：115 / 122
页数：7
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