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3V: cavity, channel and cleft volume calculator and extractor
1Department of Cell Biology, The Scripps Research Institute, CB 129, La Jolla, CA 92037, USA.
Nucleic Acids Research
|May 19, 2010
Summary
The 3V web server analyzes internal volumes in RNA and protein structures, revealing crucial clefts and cavities. This tool aids in understanding macromolecular function through detailed 3D structural analysis.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Understanding internal cavities, channels, and clefts in macromolecules like RNA and proteins is essential for elucidating their biological functions.
- The increasing availability of large macromolecular structures necessitates advanced computational tools for detailed analysis.
Purpose of the Study:
- To develop and present the 3V web server for automated extraction and comprehensive analysis of internal volumes in macromolecular structures.
- To provide researchers with a tool for investigating the functional significance of internal voids within RNA and protein molecules.
Main Methods:
- The 3V server employs a novel method based on the difference between two rolling-probe solvent-excluded surfaces with varying probe radii.
- A large probe radius identifies potential internal volumes, while a standard solvent radius (1.5 Å) defines the molecular boundary.
- This approach rapidly and accurately extracts internal volumetric data.
Main Results:
- The 3V server successfully identifies and analyzes diverse internal volumes, including deep clefts, channels, and cavities, in input RNA and protein structures.
- Volumetric data is generated as both visual representations (images) and downloadable files for further in-depth analysis.
- The server demonstrates rapid processing of structural data.
Conclusions:
- The 3V web server provides an automated and efficient solution for characterizing internal volumes in macromolecules.
- This tool facilitates a deeper understanding of structure-function relationships by enabling detailed analysis of internal cavities.
- The 3V server is a valuable resource for the structural biology and computational chemistry communities.
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