He Yi, Liwo Adam, Scheraga Harold A
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.
Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
J Chem Phys. 2015 Dec 28;143(24):243111. doi: 10.1063/1.4932082.
Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field.
粗粒度模型是研究生物分子结构和热力学性质的有用工具。它们通过将几个原子合并到一个相互作用位点而获得。这种简化模型试图在全原子表示中尽可能多地捕捉原始生物分子系统的信息，但这些粗粒度力场的所得参数仍需要进一步优化。在本文中，一种基于模拟构象集合与实验构象集合的最大似然拟合以及模拟热容量曲线与实验热容量曲线的最小二乘拟合的力场优化方法，被应用于优化我们实验室最近开发的用于核酸粗粒度模拟的核酸联合残基两点（NARES-2P）模型。优化后的NARES-2P力场比原始力场能更好地再现小DNA分子的结构和热力学数据。
