title: A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model.
abstract: Protein structure prediction is a fundamental issue in the field of computational molecular biology. In this paper, the AB off-lattice model is adopted to transform the original protein structure prediction scheme into a numerical optimization problem. We present a balance-evolution artificial bee colony (BE-ABC) algorithm to address the problem, with the aim of finding the structure for a given protein sequence with the minimal free-energy value. This is achieved through the use of convergence information during the optimization process to adaptively manipulate the search intensity. Besides that, an overall degradation procedure is introduced as part of the BE-ABC algorithm to prevent premature convergence. Comprehensive simulation experiments based on the well-known artificial Fibonacci sequence set and several real sequences from the database of Protein Data Bank have been carried out to compare the performance of BE-ABC against other algorithms. Our numerical results show that the BE-ABC algorithm is able to outperform many state-of-the-art approaches and can be effectively employed for protein structure optimization.
authors.affiliation: School of Control Science and Engineering, Zhejiang University, Hangzhou 310027, PR China; School of Advanced Engineering, Beihang University, Beijing 100191, PR China. Electronic address: libai@zju.edu.cn.
authors.forename: Bai
authors.initials: B
authors.lastname: Li
authors.affiliation: School of Design, Communication and Information Technology, The University of Newcastle, Callaghan, NSW 2308, Australia. Electronic address: Raymond.Chiong@newcastle.edu.au.
authors.forename: Raymond
authors.initials: R
authors.lastname: Chiong
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China. Electronic address: linmudl@zju.edu.cn.
authors.forename: Mu
authors.initials: M
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D001516:Bees; D032701:Biomimetics; D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D057927:Hydrophobic and Hydrophilic Interactions; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: AB off-lattice model; Amino-acid sequences; Balance-evolution artificial bee colony algorithm; Protein structure optimization