title: Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins.
abstract: Protein structure prediction (PSP) is a classical NP-hard problem in computational biology. The energy-landscape paving (ELP) method is a class of heuristic global optimization algorithm, and has been successfully applied to solving many optimization problems with complex energy landscapes in the continuous space. By putting forward a new update mechanism of the histogram function in ELP and incorporating the generation of initial conformation based on the greedy strategy and the neighborhood search strategy based on pull moves into ELP, an improved energy-landscape paving (ELP+) method is put forward. Twelve general benchmark instances are first tested on both two-dimensional and three-dimensional (3D) face-centered-cubic (fcc) hydrophobic-hydrophilic (HP) lattice models. The lowest energies by ELP+ are as good as or better than those of other methods in the literature for all instances. Then, five sets of larger-scale instances, denoted by S, R, F90, F180, and CASP target instances on the 3D FCC HP lattice model are tested. The proposed algorithm finds lower energies than those by the five other methods in literature. Not unexpectedly, this is particularly pronounced for the longer sequences considered. Computational results show that ELP+ is an effective method for PSP on the fcc HP lattice model.
authors: Jiangsu Engineering Center of Network Monitoring, Nanjing University of Information Science and Technology, Nanjing 210044, China and Network Information Center, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Jingfa
authors: J
authors: Liu
authors: Jiangsu Engineering Center of Network Monitoring, Nanjing University of Information Science and Technology, Nanjing 210044, China and School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Beibei
authors: B
authors: Song
authors: Network Information Center, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Zhaoxia
authors: Z
authors: Liu
authors: Jiangsu Engineering Center of Network Monitoring, Nanjing University of Information Science and Technology, Nanjing 210044, China and School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Weibo
authors: W
authors: Huang
authors: Jiangsu Engineering Center of Network Monitoring, Nanjing University of Information Science and Technology, Nanjing 210044, China and School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Yuanyuan
authors: Y
authors: Sun
authors: Jiangsu Engineering Center of Network Monitoring, Nanjing University of Information Science and Technology, Nanjing 210044, China and School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing 210044, China.
authors: Wenjie
authors: W
authors: Liu
mesh_terms: D000465:Algorithms; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D011506:Proteins