Using predicted shape string to enhance the accuracy of [gamma]-turn prediction

• Published in: Amino acids Vol. 42; no. 5; p. 1749
• Main Authors: Zhu, Yaojuan, Li, Tonghua, Li, Dapeng, Zhang, Yun, Xiong, Wenwei, Sun, Jiangming, Tang, Zehui, Chen, Guanyan
• Format: Journal Article
• Language: English
• Published: Vienna Springer Nature B.V 01.05.2012
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-011-0889-z

Numerous methods for predicting γ-turns in proteins have been developed. However, the results they generally provided are not very good, with a Matthews correlation coefficient (MCC) [less than or equal to]0.18. Here, an attempt has been made to develop a method to improve the accuracy of γ-turn prediction. First, we employ the geometric mean metric as optimal criterion to evaluate the performance of support vector machine for the highly imbalanced γ-turn dataset. This metric tries to maximize both the sensitivity and the specificity while keeping them balanced. Second, a predictor to generate protein shape string by structure alignment against the protein structure database has been designed and the predicted shape string is introduced as new variable for γ-turn prediction. Based on this perception, we have developed a new method for γ-turn prediction. After training and testing the benchmark dataset of 320 non-homologous protein chains using a fivefold cross-validation technique, the present method achieves excellent performance. The overall prediction accuracy Q ^sub total^ can achieve 92.2% and the MCC is 0.38, which outperform the existing γ-turn prediction methods. Our results indicate that the protein shape string is useful for predicting protein tight turns and it is reasonable to use the dihedral angle information as a variable for machine learning to predict protein folding. The dataset used in this work and the software to generate predicted shape string from structure database can be obtained from anonymous ftp site ftp://cheminfo.tongji.edu.cn/GammaTurnPrediction/ freely.