Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
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DOI：
10.1016/j.ymeth.2009.04.007
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发表时间：
2009-10
期刊：
影响因子：
4.8
通讯作者：
Otyepka, Michal
中科院分区：
文献类型：
--
作者：
Banas, Pavel;Jurecka, Petr;Walter, Nils G.;Sponer, Jiri;Otyepka, Michal
关键词：
混合QM/MM方法联合收割机结合了量子力学（QM）计算的严格性和经验分子力学（MM）处理的低计算成本，允许捕获动态特性以探测酶反应的关键原子细节。RNA酶（核酶）的催化作用直到最近才开始用QM/MM方法解决，因此仍然是一个正在开发的领域。本文综述了QM/MM应用于RNA机制的方法学和最新进展，包括HDV、发夹和锤头状核酶以及核糖体。我们比较和关联QM/MM结果与QM和/或分子动力学（MD）模拟，并讨论了范围和限制与现有的方法和计算机资源的缺点的关键眼睛。因此，我们希望促进相互欣赏，促进实验学家和理论家之间的合作，共同推进我们在原子水平上对RNA催化的理解。
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.
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影响因子：
3.3
作者：
Chen, Alan A.;Pappu, Rohit V.
通讯作者：
Pappu, Rohit V.
DOI：
10.1039/jr9580003574
发表时间：
1958-01-01
期刊：
JOURNAL OF THE CHEMICAL SOCIETY
影响因子：
--
作者：
BUNTON, CA;LLEWELLYN, DR;VERNON, CA
通讯作者：
VERNON, CA
影响因子：
1.7
作者：
BOYS, SF;BERNARDI, F
通讯作者：
BERNARDI, F
影响因子：
8.6
作者：
CAR, R;PARRINELLO, M
通讯作者：
PARRINELLO, M
影响因子：
5.7
作者：
Auffinger, P;Bielecki, L;Westhof, E
通讯作者：
Westhof, E