A novel and efficient technique for identification and classification of GPCRs.
G-protein coupled receptors (GPCRs) play a vital role in different biological processes, such as regulation of growth, death, and metabolism of cells. GPCRs are the focus of significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs. The dipeptide-based support vector machine (SVM) approach is the most accurate technique to identify and classify the GPCRs. However, this approach has two major disadvantages. First, the dimension of dipeptide-based feature vector is equal to 400. The large dimension makes the classification task computationally and memory wise inefficient. Second, it does not consider the biological properties of protein sequence for identification and classification of GPCRs. In this paper, we present a novel-feature-based SVM classification technique. The novel features are derived by applying wavelet-based time series analysis approach on protein sequences. The proposed feature space summarizes the variance information of seven important biological properties of amino acids in a protein sequence. In addition, the dimension of the feature vector for proposed technique is equal to 35. Experiments were performed on GPCRs protein sequences available at GPCRs Database. Our approach achieves an accuracy of 99.9%, 98.06%, 97.78%, and 94.08% for GPCR superfamily, families, subfamilies, and subsubfamilies (amine group), respectively, when evaluated using fivefold cross-validation. Further, an accuracy of 99.8%, 97.26%, and 97.84% was obtained when evaluated on unseen or recall datasets of GPCR superfamily, families, and subfamilies, respectively. Comparison with dipeptide-based SVM technique shows the effectiveness of our approach.
Gupta
Ravi
R
Department of Electronics and Computer Engineering, Indian Institute of Technology-Roorkee, Roorkee 247667, India. rgcsedec@iitr.ernet.in
Mittal
Ankush
A
Singh
Kuldip
K
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
D043562:Receptors, G-Protein-Coupled