American Journal of Biochemistry and Biotechnology

Low-Homology Protein Structural Class Prediction from Secondary Structure Based on Visibility and Horizontal Visibility Network

Zhi-Qin Zhao, Liang Luo and Xiao-Yan Liu

DOI : 10.3844/ajbbsp.2018.67.75

American Journal of Biochemistry and Biotechnology

Volume 14, Issue 1

Pages 67-75

Abstract

In this study, based on the predicted secondary structures of proteins, we propose a new approach to predict protein structural classes (α,β,α/β,α+β) for three widely used low-homology data sets. Fist, we obtain two time siries from the chaos game representation of each predicted secondary structure; second, based on two time series, we construct visibility and horizontal visibility network, respectively and generate a set of features using 17 network features; finaly, we predict each protein structure class using support vector machine and Fisher’s linear discriminant algorithm, respectively. In order to evaluate our method, the leave one out cross-validating test is employed on three data sets. Results show that our approach has been provided as a effective tool for the prediction of low-homology protein structural classes.

Copyright

© 2018 Zhi-Qin Zhao, Liang Luo and Xiao-Yan Liu. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.