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Updated: Jun 13, 2026
16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments
Mariusz Popenda1, Marta Szachniuk, Marek Blazewicz
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
BMC Bioinformatics
|May 13, 2010
Summary
RNA FRABASE 2.0 enhances RNA structure analysis with a powerful new database and search engine for exploring three-dimensional RNA fragments and their conformational parameters. This tool aids researchers in understanding novel RNA functions.
Area of Science:
- Structural biology
- Bioinformatics
- Computational chemistry
Background:
- Recent discoveries highlight novel RNA functions, necessitating deeper understanding of complex 3D RNA structures.
- Existing bioinformatic tools analyze RNA tertiary structures using databases like PDB and NDB.
- RNA FRABASE 1.0 was the first web-accessible database for searching 3D RNA fragments based on secondary structure patterns.
Purpose of the Study:
- To present RNA FRABASE 2.0, a significant extension of the previous version.
- To introduce novel functionalities for RNA structure analysis and data exploration.
- To provide a user-friendly platform for fast, tailored searches of 3D RNA fragments.
Main Methods:
- RNA FRABASE 2.0 incorporates data from 1565 PDB-deposited RNA structures, including NMR models.
- Its search engine utilizes an extended dot-bracket format for RNA secondary structures, accommodating multi-stranded elements and missing coordinates.
- Novel tools for advanced pattern formulation and screening of tertiary structure elements ensure high search efficiency.
Main Results:
- RNA FRABASE 2.0 offers an expanded database with novel functionalities for RNA structure analysis.
- The system provides "on the spot" structural filters and conformational parameter storage.
- Instant visualization of 3D RNA structures is integrated into the platform.
Conclusions:
- RNA FRABASE 2.0 presents a unique database and a powerful search engine with advanced features.
- The system provides comprehensive data and functionalities not available elsewhere.
- This advanced tool is expected to be valuable for researchers in the RNA field.
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