title: Structure optimization by conformational space annealing in an off-lattice protein model.
abstract: 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.
authors.affiliation: School of Computational Sciences, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul.
authors.forename: Seung-Yeon
authors.initials: SY
authors.lastname: Kim
authors.forename: Sang Bub
authors.initials: SB
authors.lastname: Lee
authors.forename: Jooyoung
authors.initials: J
authors.lastname: Lee
mesh_terms: 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
chemical_list: D011506:Proteins