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R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the
Sri Devan Appasamy1,2, Craig L Zirbel3
1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
Bioinformatics (Oxford, England)
|November 15, 2024
Summary
A new web server, R3DMCS, enables easy comparison and visualization of RNA 3D structures and motifs. This tool facilitates exploring RNA conformational changes and structural conservation across species and sequences.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Recent advancements in RNA structure determination have led to a significant increase in available 3D RNA structures.
- A gap exists in user-friendly tools for comparing and visualizing RNA motifs across these multiple 3D structures.
Purpose of the Study:
- To introduce R3DMCS, a novel browser-based web server designed for the comparison and visualization of RNA motifs within and across 3D structures.
- To provide a tool that facilitates the exploration of RNA conformational dynamics and structural conservation.
Main Methods:
- R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding nucleotides from selected RNA structures.
- The server allows comparisons across all 3D structures of a specific molecule within a species or across structures belonging to a single Rfam family.
Main Results:
- R3DMCS enables users to compare RNA motifs across diverse 3D structures, aiding in the study of conformational changes under different functional states or experimental conditions.
- The tool facilitates the investigation of 3D structure conservation across species and the impact of sequence variations on RNA structure.
Conclusions:
- R3DMCS addresses the need for an accessible tool to analyze and compare RNA 3D structural motifs.
- The server supports research into RNA structure-function relationships, conformational flexibility, and evolutionary conservation.
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