Kou S C, Oh Jason, Wong Wing Hung
Department of Statistics, Science Center, Harvard University, Cambridge, Massachusetts 02138, USA.
J Chem Phys. 2006 Jun 28;124(24):244903. doi: 10.1063/1.2208607.
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.
我们提出一种等能量（EE）采样方法，用于研究二维疏水 - 亲水（HP）晶格模型中的蛋白质折叠。这种方法能够有效地探索全局能量景观，并提供态密度的准确估计，进而使我们能够对HP蛋白质折叠的热力学进行详细研究，特别是折叠到解折叠转变的温度依赖性以及序列组成如何影响这一现象。无需额外成本，该方法还能提供全局能量最小值和基态的估计。在不使用蛋白质任何先验结构信息的情况下，EE采样器能够在大多数基准案例中找到与最知名结果相匹配的基态。数值结果表明它是研究晶格蛋白质折叠模型的一种强大方法。
