title: Extended particle swarm optimisation method for folding protein on triangular lattice.
abstract: In this study, the authors studied the protein structure prediction problem by the two-dimensional hydrophobic-polar model on triangular lattice. Particularly the non-compact conformation was modelled to fold the amino acid sequence into a relatively larger triangular lattice, which is more biologically realistic and significant than the compact conformation. Then protein structure prediction problem was abstracted to match amino acids to lattice points. Mathematically, the problem was formulated as an integer programming and they transformed the biological problem into an optimisation problem. To solve this problem, classical particle swarm optimisation algorithm was extended by the single point adjustment strategy. Compared with square lattice, conformations on triangular lattice are more flexible in several benchmark examples. They further compared the authors' algorithm with hybrid of hill climbing and genetic algorithm. The results showed that their method was more effective in finding solution with lower energy and less running time.
authors.affiliation: Department of Mathematics, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China. guoyuzhen1980@163.com.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Business School, University of Shanghai for Science and Technology, Shanghai, People's Republic of China.
authors.forename: Zikai
authors.initials: Z
authors.lastname: Wu
authors.affiliation: School of Science, Dalian Jiaotong University, Dalian, People's Republic of China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D011506:Proteins
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