Prediction of G-protein-coupled receptor classes based on the concept of Chou’s pseudo amino acid composition: An approach from discrete wavelet transform

• Published in: Analytical biochemistry 2009-07, Vol.390 (1), p.68-73
• Main Authors: Qiu, Jian-Ding, Huang, Jian-Hua, Liang, Ru-Ping, Lu, Xiao-Quan
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acids - chemistry; Artificial Intelligence; Discrete wavelet transform; G-protein-coupled receptors; Hydrophobic and Hydrophilic Interactions; Hydrophobicity scale; Pseudo amino acid composition; Receptors, G-Protein-Coupled - chemistry; Receptors, G-Protein-Coupled - classification; Support vector machine
• ISSN: 0003-2697; 1096-0309
• DOI: 10.1016/j.ab.2009.04.009

Being the largest family of cell surface receptors, G-protein-coupled receptors (GPCRs) are among the most frequent targets. The functions of many GPCRs are unknown, and it is both time-consuming and expensive to determine their ligands and signaling pathways by experimental methods. It is of great practical significance to develop an automated and reliable method for classification of GPCRs. In this study, a novel method based on the concept of Chou’s pseudo amino acid composition has been developed for predicting and recognizing GPCRs. The discrete wavelet transform was used to extract feature vectors from the hydrophobicity scales of amino acid to construct pseudo amino acid (PseAA) composition for training support vector machine. The prediction accuracies by the current method among the major families of GPCRs, subfamilies of class A, and types of amine receptors were 99.72%, 97.64%, and 99.20%, respectively, showing 9.4% to 18.0% improvement over other existing methods and indicating that the proposed method is a useful automated tool in identifying GPCRs.