Protein folding on the hexagonal lattice in the HP model.
In this paper, we introduce the 2D hexagonal lattice as a biologically meaningful alternative to the standard square lattice for the study of protein folding in the HP model. We show that the hexagonal lattice alleviates the "sharp turn" problem and models certain aspects of the protein secondary structure more realistically. We present a 1/6-approximation and a clustering heuristic for protein folding on the hexagonal lattice. In addition to these two algorithms, we also implement a Monte Carlo Metropolis algorithm and a branch-and-bound partial enumeration algorithm, and conduct experiments to compare their effectiveness.
Jiang
Minghui
M
Department of Computer Science, Montana State University, Bozeman, Montana 59717-3880, USA. jiang@cs.montana.edu
Zhu
Binhai
B
D000465:Algorithms; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
D011506:Proteins