title: Protein-folding simulations of the hydrophobic-hydrophilic model by combining pull moves with energy landscape paving.
abstract: The energy landscape paving (ELP) method is a class of heuristic global optimization algorithms based on Monte Carlo sampling. By incorporating the generation of an initial conformation based on a greedy strategy, the conformation update mechanism based on pull moves, and some heuristic off-trap strategies into an improved ELP method, we propose an alternative version of the ELP method, called the ELP-pull move method. We test the ELP-pull move method on both two-dimensional (2D) and 3D hydrophobic-hydrophilic protein-folding models. For ten 2D benchmark sequences of length ranging from 20 to 100, the proposed algorithm finds the lowest energies so far. Within the achieved results, the algorithm converges more rapidly and efficiently than previous methods. For all ten 3D sequences with a length of 64, the ELP-pull move method finds lower energies within comparable computational times. The numerical results demonstrate that our algorithm is a powerful method to study the lattice protein-folding model.
authors: School of Computer & Software, Nanjing University of Information Science & Technology, Nanjing 210044, China. jfliu@nuist.edu.cn
authors: Jingfa
authors: J
authors: Liu
authors: Gang
authors: G
authors: Li
authors: Jun
authors: J
authors: Yu
mesh_terms: D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D013314:Stress, Mechanical; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water