A Sequence-based Approach for Predicting Protein Disordered Regions

Tao      Huang; Zhi-Song      He; Wei-Ren      Cui; Yu-Dong      Cai; Xiao-He      Shi; Le-Le      Hu; Kuo-Chen      Chou

doi:10.2174/0929866511320030002

Abstract

Protein disordered regions are associated with some critical cellular functions such as transcriptional regulation, translation and cellular signal transduction, and they are responsible for various diseases. Although experimental methods have been developed to determine these regions, they are time-consuming and expensive. Therefore, it is highly desired to develop computational methods that can provide us with this kind information in a rapid and inexpensive manner. Here we propose a sequence-based computational approach for predicting protein disordered regions by means of the Nearest Neighbor algorithm, in which conservation, amino acid factor and secondary structure status of each amino acid in a fixed-length sliding window are taken as the encoding features. Also, the feature selection based on mRMR (maximum Relevancy Minimum Redundancy) is applied to obtain an optimal 51-feature set that includes 39 conservation features and 12 secondary structure features. With the optimal 51 features, our predictor yielded quite promising MCC (Mathew's correlation coefficients): 0.371 on a rigorous benchmark dataset tested by 5-fold cross-validation and 0.219 on an independent test dataset. Our results suggest that conservation and secondary structure play important roles in intrinsically disordered proteins.

Keywords: Feature space, mRMR, sliding window, intrinsically disordered proteins, nearest neighbor algorithm, amino acid factor, conservation score, signal transduction, translation, regulation