A new hybrid coding for protein secondary structure prediction based on primary structure similarity.
The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the physicochemical properties of amino acids to construct a 3-bit-code, and then the 3 tendency factors of amino acids are calculated to generate another 3-bit-code. Two 3-bit-codes are fused to form a novel hybrid 6-bit-code. Furthermore, we make a geometry-based similarity comparison of the protein primary structure between the reference set and the test set before the secondary structure prediction. We finally use the support vector machine (SVM) to predict those amino acids which are not detected by the primary structure similarity comparison. Experimental results show that our method achieves a satisfactory improvement in accuracy in the prediction of protein secondary structure.
College of Science, Zhejiang Sci-Tech University, Hangzhou 30018, China. Electronic address: lizhong@zstu.edu.cn.
Zhong
Z
Li
College of Science, Zhejiang Sci-Tech University, Hangzhou 30018, China.
Jing
J
Wang
Department of Statistics, University of Central Florida, Orlando 32816, USA.
Shunpu
S
Zhang
College of Science, Zhejiang Sci-Tech University, Hangzhou 30018, China.
Qifeng
Q
Zhang
College of Science, Zhejiang Sci-Tech University, Hangzhou 30018, China.
Wuming
W
Wu
D000596:Amino Acids / Q000737:chemistry; D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D060388:Support Vector Machine
D000596:Amino Acids
Hybrid code; Protein primary structure; Protein secondary structure prediction; Support vector machine