Physics-based RNA structure prediction.
Physics-based RNA structure prediction.
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DOI：
10.1007/s41048-015-0001-4
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发表时间：
2015
影响因子：
--
通讯作者：
Chen SJ
中科院分区：
文献类型：
--
作者：
Xu X;Chen SJ
尽管简单短RNA的二级结构预测取得了成功，但预测具有长距离三级折叠的RNA的问题仍然存在。此外，RNA的三维结构预测受到缺乏有关三级接触及其热力学参数的知识的阻碍。低分辨率结构建模使我们能够通过严格的统计力学计算来估计一些三级褶皱的构象熵。该模型导致在粗粒度水平的三维第三次褶皱。粗粒度结构作为初始结构进行全原子分子动力学精化，以构建最终的全原子3D结构。本文综述了RNA二级和三级结构预测的计算模型，重点介绍了最近发展起来的RNA统计力学模型--Vfold模型。主要的重点放在模型背后的物理，包括二级和三级结构建模中的非典型相互作用的处理，以及与RNA功能的相关性。
Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions.