title: Structure optimization in a three-dimensional off-lattice protein model.
abstract: We studied a three-dimensional off-lattice AB model with two species of monomers, hydrophobic (A) and hydrophilic (B), and present two optimization algorithms: face-centered-cubic (FCC)-lattice pruned-enriched-Rosenbluth method (PERM) and subsequent conjugate gradient (PERM++) minimization and heuristic conjugate gradient (HCG) simulation based on "off-trap" strategy. In PERM++, we apply the PERM to the FCC-lattice to produce the initial conformation, and conjugate gradient minimization is then used to reach the minimum energy state. Both algorithms have been tested in the three-dimensional AB model for all sequences with lengths 13 < or = n < or = 55. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we renew the putative ground states energy values.
authors.affiliation: School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Wenqi
authors.initials: W
authors.lastname: Huang
authors.forename: Jingfa
authors.initials: J
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins; D013816:Thermodynamics
chemical_list: D011506:Proteins