通过对全原子力场进行简单的范德华校正来预测RNA结构。
Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field.
作者信息
Yang Changwon, Lim Manho, Kim Eunae, Pak Youngshang
机构信息
Department of Chemistry and Institute of Functional Materials, Pusan National University , Busan 46241, South Korea.
College of Pharmacy, Chosun University , Gwangju 61452, South Korea.
出版信息
J Chem Theory Comput. 2017 Feb 14;13(2):395-399. doi: 10.1021/acs.jctc.6b00808. Epub 2017 Jan 3.
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.
我们通过不等的洛伦兹 - 贝特洛组合规则，对AMBER ff12力场提出了一种简单的范德华主链校正（O2'和OP），并结合OPC水模型。在四种不同的四核苷酸如r(GACC)、r(CCCC)、r(AAAA)和r(CAAU)上进行测试时，这种新的力场正确地将每个天然折叠捕获为最大丰度构象。对于所测试的RNA四环（UUCG），其天然折叠的稳定性得到了显著提高。
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