Using adaptive K-nearest neighbor algorithm and cellular automata images to predicting G-Protein-Coupled Receptor classes

Interdisciplinary Sciences, Computational Life Sciences
Xuan Xiao, Wang-Ren Qiu

Abstract

G-Protein-Coupled Receptors (GPCRs) are the largest of cell surface receptor, accounting for >1% of the human genome. They play a key role in cellular signaling networks that regulate various physiological processes. The functions of many of GPCRs are unknown, because they are difficult to crystallize and most of them will not dissolve in normal solvents. This difficulty has motivated and challenged the development of a computational method which can predict the classification of the families and subfamilies of GPCRs based on their primary sequence so as to help us classify drugs. In this paper the adaptive K-nearest neighbor algorithm and protein cellular automata image (CAI) is introduced. Based on the CAI, the complexity measure factors derived from each of the protein sequences concerned are adopted for its Pseudo amino acid composition. GPCRs were categorized into nine subtypes. The overall success rate in identifying GPCRs among their nine family classes was about 83.5%. The high success rate suggests that the adaptive K-nearest neighbor algorithm and protein CAI holds very high potential to become a useful tool for understanding the actions of drugs that target GPCRs and designing new medications with fewer side effects ...Continue Reading

References

Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Apr 9, 1999·Protein Engineering·K C Chou, D W Elrod
Mar 21, 2003·Journal of Proteome Research·Kuo-Chen Chou, David W Elrod
Jun 28, 2005·Nucleic Acids Research·Manoj Bhasin, G P S Raghava
Aug 9, 2005·Journal of Proteome Research·Kuo-Chen Chou
Oct 13, 2006·Protein Engineering, Design & Selection : PEDS·Qing-Bin Gao, Zheng-Zhi Wang
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Nov 28, 2008·Journal of Computational Chemistry·Xuan XiaoKuo-Chen Chou

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