Structure optimization by conformational space annealing in an off-lattice protein model.
The optimization results by conformational space annealing are presented for an off-lattice protein model consisting of hydrophobic and hydrophilic residues in Fibonacci sequences. The ground-state energies found are lower than those reported in the literature. In addition, the ground-state conformations in three dimensions exhibit the important aspect of forming a single hydrophobic core in real proteins. The energy landscape for the population of local minima is also investigated.
Kim
Seung-Yeon
SY
School of Computational Sciences, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul.
Lee
Sang Bub
SB
Lee
Jooyoung
J
D000465:Algorithms; D055592:Biophysical Phenomena; D001703:Biophysics; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism; D013696:Temperature
D011506:Proteins