RNAscape: geometric mapping and customizable visualization of RNA structure.
RNAscape: geometric mapping and customizable visualization of RNA structure.
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RNAscape：RNA 结构的几何映射和可定制可视化。
DOI：
10.1093/nar/gkae269
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发表时间：
2024
影响因子：
14.9
通讯作者：
Rohs,Remo
中科院分区：
文献类型：
--
作者：
Mitra,Raktim;Cohen,AriS;Rohs,Remo
分析和可视化RNA的三级结构和复杂的相互作用对于能够机械地破译其在体内的分子功能是必不可少的。二级结构可视化软件可以描绘RNA的许多方面；然而，这些布局往往无法保持拓扑对应，因为它们不考虑RNA分子不同区域之间的三级相互作用。同样，二级结构可视化工具也不考虑两个或多个相互作用的RNA分子之间的四级相互作用。RNAscape web服务器生成的可视化可以保持拓扑对应，同时保持视觉上的直观和结构上的洞察力。RNAscape通过设计一个数学结构映射算法来实现这一目标，该算法优先考虑螺旋段，反映它们的三级组织。非螺旋段以最小化结构杂波的方式进行映射。RNAscape运行一个绘图脚本，用于生成出版质量的图像。RNAscape原生支持非标准核苷酸、多碱基配对注释样式，不需要编程经验。RNAscape还可用于分析RNA/DNA杂交结构和DNA拓扑结构，包括g -四联体。用户可以上传自己的三维结构或输入现有结构的蛋白质数据库（PDB） ID。RNAscape web服务器允许用户根据需要通过各种设置自定义可视化。URL: https://rnascape.usc.edu/。
Analyzing and visualizing the tertiary structure and complex interactions of RNA is essential for being able to mechanistically decipher their molecular functionsin vivo. Secondary structure visualization software can portray many aspects of RNA; however, these layouts are often unable to preserve topological correspondence since they do not consider tertiary interactions between different regions of an RNA molecule. Likewise, quaternary interactions between two or more interacting RNA molecules are not considered in secondary structure visualization tools. The RNAscape webserver produces visualizations that can preserve topological correspondence while remaining both visually intuitive and structurally insightful. RNAscape achieves this by designing a mathematical structural mapping algorithm which prioritizes the helical segments, reflecting their tertiary organization. Non-helical segments are mapped in a way that minimizes structural clutter. RNAscape runs a plotting script that is designed to generate publication-quality images. RNAscape natively supports non-standard nucleotides, multiple base-pairing annotation styles and requires no programming experience. RNAscape can also be used to analyze RNA/DNA hybrid structures and DNA topologies, including G-quadruplexes. Users can upload their own three-dimensional structures or enter a Protein Data Bank (PDB) ID of an existing structure. The RNAscape webserver allows users to customize visualizations through various settings as desired. URL: https://rnascape.usc.edu/.