用嵌套蒙特卡罗搜索求解HP模型
Solving the HP model with Nested Monte Carlo Search
摘要：
在本文中，我们提出了一种新的蒙特卡罗搜索（MCS）算法，用于寻找蛋白质的基态能量的HP模型。我们还简要地比较了其他MCS算法通常不使用的HP模型，并提供了一个概述的算法上HP模型。本文中提出的算法没有击败最先进的算法，请参阅PERM（Hsu和Grassberger 2011），REMC（Thachuk，Shmygelska和Hoos 2007）或WLRE（Wüst和Landau 2012）以获得更好的结果。徐，H.- P的; and Grassberger，P. 2011.用PERM对聚合物进行蒙特卡罗模拟的综述。Journal of Statistical Physics，144（3）：597 to 637. Thachuk，C.; Shmygelska，A.;和Hoos，H. H. 2007. HP模型中蛋白质折叠的副本交换蒙特卡罗算法。BMC Bioinformatics，8（1）：342. Wüst，T.;和Landau，D. P. 2012.晶格聚合物的优化Wang-Landau采样：HP模型蛋白质的基态搜索和折叠热力学。化学物理学报，137（6）：064903.
英文摘要：
In this paper we present a new Monte Carlo Search (MCS) algorithm for finding the ground state energy of proteins in the HP-model. We also compare it briefly to other MCS algorithms not usually used on the HP-model and provide an overview of the algorithms used on HP-model. The algorithm presented in this paper does not beat state of the art algorithms, see PERM (Hsu and Grassberger 2011), REMC (Thachuk, Shmygelska, and Hoos 2007) or WLRE (Wüst and Landau 2012) for better results. Hsu, H.-P.; and Grassberger, P. 2011. A review of Monte Carlo simulations of polymers with PERM. Journal of Statistical Physics, 144 (3): 597 to 637. Thachuk, C.; Shmygelska, A.; and Hoos, H. H. 2007. A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinformatics, 8(1): 342. Wüst, T.; and Landau, D. P. 2012. Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins. The Journal of Chemical Physics, 137(6): 064903.
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