Improved prediction of RNA tertiary structure with insights into native state dynamics
Improved prediction of RNA tertiary structure with insights into native state dynamics
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DOI：
10.1261/rna.027201.111
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发表时间：
2012-03-01
期刊：
影响因子：
4.5
通讯作者：
Maher, L. James, III
中科院分区：
文献类型：
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作者：
Bida, John Paul;Maher, L. James, III
RNA分子的高分辨核磁共振和X-射线晶体结构的发表数量越来越多，证明了RNA三级结构的重要性。这些结构提供了对功能的洞察，并创建了一个知识库，该知识库可由ASSEMBLE、MARDNA、RNABuilder、NAST、FARNA、Mc-Sym、RNA2D3D和iFoldRNA等程序用于三级结构预测和设计。虽然这些方法在模拟过程中对天然的RNA结构进行采样，但都在得分后努力捕捉天然的RNA构象。我们提出了一种改进的RNA片段组装方法RSIM，该方法在采样构象的同时保留了RNA的整体二级结构。这种方法提高了预测的RNA三级结构的质量，提供了对本征状态动力学的洞察，并生成了对RNA构象空间的强大可视化。Rsim可从http://www.github.com/jpbida/rsim.下载
The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from http://www.github.com/jpbida/rsim.