title: A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling.
abstract: We propose an equi-energy (EE) sampling approach to study protein folding in the two-dimensional hydrophobic-hydrophilic (HP) lattice model. This approach enables efficient exploration of the global energy landscape and provides accurate estimates of the density of states, which then allows us to conduct a detailed study of the thermodynamics of HP protein folding, in particular, on the temperature dependence of the transition from folding to unfolding and on how sequence composition affects this phenomenon. With no extra cost, this approach also provides estimates on global energy minima and ground states. Without using any prior structural information of the protein the EE sampler is able to find the ground states that match the best known results in most benchmark cases. The numerical results demonstrate it as a powerful method to study lattice protein folding models.
authors.affiliation: Department of Statistics, Science Center, Harvard University, Cambridge, Massachusetts 02138, USA. kou@stat.harvard.edu
authors.forename: S C
authors.initials: SC
authors.lastname: Kou
authors.forename: Jason
authors.initials: J
authors.lastname: Oh
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods*; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins