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Updated: Mar 3, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
DSSR-enhanced visualization of nucleic acid structures in Jmol
Robert M Hanson1, Xiang-Jun Lu2
1Department of Chemistry, St. Olaf College, Northfield, MN 55057, USA.
Dissecting the Spatial Structure of RNA (DSSR) now integrates with Jmol and JSmol, enhancing RNA 3D structure visualization and analysis. This tool provides detailed structural features, improving RNA bioinformatics capabilities.
Area of Science:
- Structural Bioinformatics
- Molecular Visualization
- RNA Biology
Background:
- Sophisticated visualization is crucial for understanding macromolecular 3D structures.
- RNA structural bioinformatics tools currently lack comprehensive visualization features for RNA-specific elements like base pairs and hairpin loops.
- Existing molecular graphics tools often do not support detailed RNA structural analysis.
Purpose of the Study:
- To integrate Dissecting the Spatial Structure of RNA (DSSR) with Jmol and JSmol for enhanced RNA 3D structure visualization.
- To provide accessible analysis of RNA structural features comparable to protein visualization.
- To fill a gap in RNA structural bioinformatics by enabling deeper analysis of structural characteristics.
Main Methods:
- Integration of DSSR, a command-line tool for RNA structure analysis, with Jmol (Java) and JSmol (JavaScript) viewers.
- Development of a DSSR web service accepting PDB or mmCIF files from Jmol/JSmol sessions.
- Outputting DSSR-derived structural features in JSON format for web-based visualization.
Main Results:
- DSSR features are now accessible through both Jmol and JSmol applications.
- A seamless workflow allows users to initiate analysis from Jmol/JSmol and receive DSSR features.
- The integration brings RNA 3D structure visualization and analysis capabilities to a level comparable to protein structures.
Conclusions:
- The DSSR-Jmol/JSmol integration significantly advances RNA structural bioinformatics.
- This tool enables deeper analysis and better understanding of complex RNA 3D structures.
- The freely accessible resource enhances web-based visualization and analysis of RNA structures.
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