title: The simulation of the three-dimensional lattice hydrophobic-polar protein folding.
abstract: One of the most prominent problems in computational biology is to predict the natural conformation of a protein from its amino acid sequence. This paper focuses on the three-dimensional hydrophobic-polar (HP) lattice model of this problem. The modified elastic net (EN) algorithm is applied to solve this nonlinear programming hard problem. The lattice partition strategy and two local search methods (LS(1) and LS(2)) are proposed to improve the performance of the modified EN algorithm. The computation and analysis of 12 HP standard benchmark instances are also involved in this paper. The results indicate that the hybrid of modified EN algorithm, lattice partition strategy, and local search methods has a greater tendency to form a globular state than genetic algorithm does. The results of noncompact model are more natural in comparison with that of compact model.
authors.affiliation: Department of Applied Mathematics, Dalian University of Technology, Dalian, 116024, People's Republic of China. guoyuzhen1980@163.com
authors.forename: Yu-Zhen
authors.initials: YZ
authors.lastname: Guo
authors.forename: En-Min
authors.initials: EM
authors.lastname: Feng
mesh_terms: D000465:Algorithms; D055592:Biophysical Phenomena; D001703:Biophysics; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004548:Elasticity; D008957:Models, Genetic; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins