Classifying G-protein coupled receptors with bagging classification tree

Authors:
Ying Huang;Jun Cai;Liang Ji;Yanda Li
Affiliations:
Department of Automation, MOE Key Laboratory of Bioinformatics, Institute of Bioinformatics, Tsinghua University, Beijing 10084, China;Department of Automation, MOE Key Laboratory of Bioinformatics, Institute of Bioinformatics, Tsinghua University, Beijing 10084, China;Department of Automation, MOE Key Laboratory of Bioinformatics, Institute of Bioinformatics, Tsinghua University, Beijing 10084, China;Department of Automation, MOE Key Laboratory of Bioinformatics, Institute of Bioinformatics, Tsinghua University, Beijing 10084, China
Venue:
Computational Biology and Chemistry
Year:
2004

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Abstract

G-protein coupled receptors (GPCRs) play a key role in different biological processes, such as regulation of growth, death and metabolism of cells. They are major therapeutic targets of numerous prescribed drugs. However, the ligand specificity of many receptors is unknown and there is little structural information available. Bioinformatics may offer one approach to bridge the gap between sequence data and functional knowledge of a receptor. In this paper, we use a bagging classification tree algorithm to predict the type of the receptor based on its amino acid composition. The prediction is performed for GPCR at the sub-family and sub-sub-family level. In a cross-validation test, we achieved an overall predictive accuracy of 91.1% for GPCR sub-family classification, and 82.4% for sub-sub-family classification. These results demonstrate the applicability of this relative simple method and its potential for improving prediction accuracy.