Structure optimization in a three-dimensional off-lattice protein model.
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.
Huang
Wenqi
W
School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
Liu
Jingfa
J
D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins; D013816:Thermodynamics
D011506:Proteins