Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
复制标题
通过分子间相互作用验证核酸的极化力场参数
DOI：
10.1007/s11705-016-1572-4
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发表时间：
2016-05
影响因子：
4.5
通讯作者：
Li Guohui
中科院分区：
文献类型：
--
作者：
Cao Liaoran;Ren Hong;Miao Jing;Guo Wei;Li Yan;Li Guohui
Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.
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DOI：
10.1021/jp408909t
发表时间：
2014-02-06
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Condon DE;Yildirim I;Kennedy SD;Mort BC;Kierzek R;Turner DH
通讯作者：
Turner DH
影响因子：
3.3
作者：
Pengyu Y. Ren;J. Ponder
通讯作者：
Pengyu Y. Ren;J. Ponder
影响因子：
3
作者：
Vanommeslaeghe, K.;Hatcher, E.;Acharya, C.;Kundu, S.;Zhong, S.;Shim, J.;Darian, E.;Guvench, O.;Lopes, P.;Vorobyov, I.;MacKerell, A. D., Jr.
通讯作者：
MacKerell, A. D., Jr.
DOI：
10.1002/0471433519.ch3
发表时间：
2003-02
期刊：
--
影响因子：
--
作者：
S. Rick;S. Stuart
通讯作者：
S. Rick;S. Stuart
影响因子：
4.4
作者：
Izvekov, S;Parrinello, M;Voth, GA
通讯作者：
Voth, GA