Identifying GPCRs and their Types with Chou’s Pseudo Amino Acid Composition: An Approach from Multi-scale Energy Representation and Position Specific Scoring Matrix

Zia-ur-Rehman; Asifullah      Khan

Abstract

G-protein coupled receptor (GPCR) is a membrane protein family, which serves as an interface between cell and the outside world. They are involved in various physiological processes and are the targets of more than 50% of the marketed drugs. The function of GPCRs can be known by conducting Biological experiments. However, the rapid increase of GPCR sequences entering into databanks, it is very time consuming and expensive to determine their function based only on experimental techniques. Hence, the computational prediction of GPCRs is very much demanding for both pharmaceutical and educational research. Feature extraction of GPCRs in the proposed research is performed using three techniques i.e. Pseudo amino acid composition, Wavelet based multi-scale energy and Evolutionary information based feature extraction by utilizing the position specific scoring matrices. For classification purpose, a majority voting based ensemble method is used; whose weights are optimized using genetic algorithm. Four classifiers are used in the ensemble i.e. Nearest Neighbor, Probabilistic Neural Network, Support Vector Machine and Grey Incidence Degree. The performance of the proposed method is assessed using Jackknife test for a number of datasets. First, the individual performances of classifiers are assessed for each dataset using Jackknife test. After that, the performance for each dataset is improved by using weighted ensemble classification. The weights of ensemble are optimized using various runs of Genetic Algorithm. We have compared our method with various other methods. The significance in performance of the proposed method depicts it to be useful for GPCRs classification.

Keywords: Grey incidence degree, GPCR prediction, nearest neighbor, position specific scoring matrix, probabilistic neural network, support vector machine, G-protein coupled receptors (GPCRs), alpha helical domains, extracellular loops, allergies