R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

Bioinformatics (Oxford, England) Pub Date : 2024-11-01 DOI:10.1093/bioinformatics/btae682

Sri Devan Appasamy, Craig L Zirbel

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Abstract

Motivation: The recent progress in RNA structure determination methods has resulted in a surge of newly solved RNA 3D structures. However, there is an absence of a user-friendly browser-based tool that can facilitate the comparison and visualization of RNA motifs across multiple 3D structures.

Results: We introduce R3DMCS, a web server that allows users to compare selected RNA nucleotides across all 3D structures of a given molecule from a given species, or across all 3D structures mapped to a single Rfam family. Starting from one instance of the motif, R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures. With R3DMCS, one can explore conformational changes of motifs due to 3D structures being solved in different functional states or different experimental conditions. One can also investigate conservation of 3D structure across species, or changes in 3D structure due to changes in sequence.

Availability and implementation: R3DMCS is open-source software and freely available at https://rna.bgsu.edu/correspondence/ and https://github.com/BGSU-RNA/RNA-3D-correspondence.

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R3DMCS：网络服务器，用于可视化来自同一生物体或不同物种的实验三维结构中的 RNA 主题结构变化。

动机最近在 RNA 结构测定方法方面取得的进展导致新解决的 RNA 三维结构激增。然而，目前还没有一种基于浏览器的用户友好型工具，可以方便地对多个三维结构中的 RNA 主题进行比较和可视化：我们介绍了 R3DMCS，它是一个网络服务器，用户可以通过该服务器比较特定物种特定分子所有三维结构中的选定 RNA 核苷酸，或比较映射到单个 Rfam 家族的所有三维结构中的选定 RNA 核苷酸。R3DMCS 从一个主题实例开始，检索、对齐、注释、组织和显示其他三维结构中相应核苷酸集的三维坐标。利用 R3DMCS，人们可以探索三维结构在不同功能状态或不同实验条件下的构象变化。还可以研究不同物种间三维结构的保持情况，或因序列变化而导致的三维结构变化：R3DMCS 是开源软件，可在 https://rna.bgsu.edu/correspondence/ 和 https://github.com/BGSU-RNA/RNA-3D-correspondence 免费获取：补充数据可在 Bioinformatics online 上获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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