Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings
Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings
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DOI：
10.1021/acs.jctc.5b00200
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发表时间：
2015-07-01
影响因子：
5.5
通讯作者：
Pasquali, Samuela
中科院分区：
文献类型：
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作者：
Cragnolini, Tristan;Laurin, Yoann;Pasquali, Samuela
HIRE-RNA是一个用于RNA结构预测和RNA折叠动力学研究的粗略模型。通过使用简化的粒子集和详细的相互作用来解释碱基配对和堆叠，我们表明非规范和多重碱基相互作用对于捕获复杂rna的完整物理行为是必要的。在本文中，我们给出了完整的模型，并给出了16个体系的折叠、稳定性和自由能表面的结果，这些体系具有12到76个核苷酸，结构越来越复杂，从单体到二聚体，总共使用850 μ s的模拟时间。
HIRE-RNA is a coarse-gtained model for RNA structure prediction and the dynamical study of RNA folding. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking, we show that noncanonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper, we give a full account of the model and present results on the folding, stability, and free energy Surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850 mu s of simulation time.