Elastic Network Models of Nucleic Acids Flexibility.
Elastic Network Models of Nucleic Acids Flexibility.
复制标题
核酸灵活性的弹性网络模型
DOI：
10.1021/ct400814n
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发表时间：
2013
影响因子：
5.5
通讯作者：
Zacharias M.
中科院分区：
文献类型：
--
作者：
Setny P;Zacharias M.
弹性网络模型（ENMs）是描述蛋白质系统大规模运动的有效工具。虽然它们在蛋白质的背景下得到了很好的验证，但对于它们对核酸的适用性知之甚少，它们的不同结构不一定保证具有可比的性能。在这项研究中，我们全面评估和优化了流行的enm捕获RNA和DNA灵活性的效率。我们还介绍了两种可选模型，其中粗粒度级别的弹性连接强度由原子分辨率的距离分布控制。对于每个考虑的enm，我们报告了弹簧连接的最佳长度以及弹性力常数的缩放，这些常数提供了基于原子力场的振动频率与正模态的最佳一致性。为了确定力常数的绝对值，提出了一种基于Hessian矩阵伪逆重叠的新方法。
Elastic network models (ENMs) are a useful tool for describing large scale motions in protein systems. While they are well validated in the context of proteins, relatively little is known about their applicability to nucleic acids, whose different architecture does not necessarily warrant comparable performance. In this study we thoroughly evaluate and optimize the efficiency of popular ENMs for capturing RNA and DNA flexibility. We also introduce two alternative models in which the strength of elastic connections at a coarse-grained level is governed by distance distribution at atomic resolution. For each of the considered ENMs we report the optimal length of spring connections as well as the scaling of elastic force constants that provides the best agreement of vibrational frequencies with normal modes based on atomic force field. In order to determine the absolute values of force constants we introduce a novel method based on the overlap of pseudoinverse of Hessian matrices.
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影响因子：
3
作者：
Setny P;Bahadur RP;Zacharias M
通讯作者：
Zacharias M
影响因子：
5.6
作者：
Bahar, I;Jernigan, RL
通讯作者：
Jernigan, RL
分子柔性对 DNA 放射敏感性的影响：模拟研究。
DOI：
--
发表时间：
2000
期刊：
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
影响因子：
--
作者：
D. Viduna;K. Hinsen;G. Kneller
通讯作者：
G. Kneller
影响因子：
3
作者：
Wang, YM;Rader, AJ;Jernigan, RL
通讯作者：
Jernigan, RL
影响因子：
16.6
作者：
Rohs R;Jin X;West SM;Joshi R;Honig B;Mann RS
通讯作者：
Mann RS