Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field

被引：34

作者：

Yang, Changwon ^{[1
,2
]}

Lim, Manho ^{[1
,2
]}

Kim, Eunae ^{[3
]}

Pak, Youngshang ^{[1
,2
]}

机构：

[1] Pusan Natl Univ, Dept Chem, Busan 46241, South Korea

[2] Pusan Natl Univ, Inst Funct Mat, Busan 46241, South Korea

[3] Chosun Univ, Coll Pharm, Gwangju 61452, South Korea

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2017年 / 13卷 / 02期

基金：

新加坡国家研究基金会;

关键词：

FREE-ENERGY LANDSCAPE; MOLECULAR-DYNAMICS; TETRALOOPS; METADYNAMICS; PARAMETERS; SIMULATIONS; PROTEINS; TORSIONS; WATER; FOLD;

D O I：

10.1021/acs.jctc.6b00808

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We proposed a simple van der Waals backbone correction (O2' and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal Lorentz-Berthelot combination rule. As tested on four different tetranuceotides such as r(GACC), r(CCCC), r(AAAA), and r(CAAU), this new force field correctly captured each native fold as the largest population. For a RNA tetraloop (UUCG) tested, the stability of its native fold is substantially improved.

引用

页码：395 / 399

页数：5

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