Energy optimization for off-lattice protein folding.
Two three-dimensional AB off-lattice protein models consisting of hydrophobic and hydrophilic monomers are studied in this paper. By incorporating an extra energy contribution into the original energy function, the protein folding is converted from a constraint optimization problem into an unconstrained one which can be solved by the well-known gradient method. From the initial configurations randomly generated by the heuristic strategy proposed in this paper, our algorithm can find better results than those by nPERM for the four Fibonacci sequences. Based on the initial configurations obtained by energy landscape paving (ELP) routine, some of our results for the lowest energies are better than the best values reported in the literature.
Huang
Wenqi
W
School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
Chen
Mao
M
Lü
Zhipeng
Z
D003198:Computer Simulation; D004735:Energy Transfer; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013816:Thermodynamics
D011506:Proteins