Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
RNA. 2012 Mar;18(3):385-93. doi: 10.1261/rna.027201.111. Epub 2012 Jan 25.
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.
从越来越多发表的 RNA 分子高分辨率 NMR 和 X 射线晶体结构可以明显看出 RNA 三级结构的重要性。这些结构提供了对功能的深入了解，并为 Assemble、ModeRNA、RNABuilder、NAST、FARNA、Mc-Sym、RNA2D3D 和 iFoldRNA 等程序创建了知识库，这些程序可用于三级结构预测和设计。虽然这些方法在模拟过程中采样类似天然的 RNA 结构，但在评分后，所有方法都难以捕获天然 RNA 构象。我们提出了 RSIM，这是一种改进的 RNA 片段组装方法，可在采样构象的同时保留 RNA 的全局二级结构。这种方法可以提高预测 RNA 三级结构的质量，深入了解天然状态的动力学，并生成 RNA 构象空间的强大可视化效果。RSIM 可从 http://www.github.com/jpbida/rsim 下载。
