A Hybrid Algorithm Based on Artificial Bee Colony and Pigeon Inspired Optimization for 3D Protein Structure Prediction

摘要

With the accomplishment of the Human Genome Project, the significance of protein structure research becomes more outstanding. The prediction of protein structure is aimed at the study of amino acid molecules, and belongs to the field of Bio-Nano research. There are two kinds of methodsto study protein structure: experiment and theory. This paper adopts ab-initio prediction method which is one of theoretical methods. Based on the "thermodynamic hypothesis," there are many different models applied to the field. This paper selects 3D AB off-lattice model to solve thisproblem. ABC-PIO combines the characteristics of the diversity generated by artificial bee colony algorithm and the fast convergence speed of pigeon inspired optimization. At the end of this algorithm, Cauchy perturbation strategy is added to optimize the local optimum. Two functions are introducedto dynamically control two operators of the hybrid algorithm. In order to test the quality of ABC-PIO, ten real protein sequences from the Protein Data Bank have been selected. Compared with other four algorithms, the algorithm gets better result. To calculate the error between the predictedand the true protein structure RMSD is set. Comparisons are made not only in the convergence curves but also in the backbone drawings.