3V: cavity, channel and cleft volume calculator and extractor

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W555-62. doi: 10.1093/nar/gkq395. Epub 2010 May 16.


As larger macromolecular structures become available, there is a growing need to understand their 'internal' volumes--such as deep clefts, channels and cavities--as these often play critical roles in their function. The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures. It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 A for water). The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis. The 3V server and source code are available from http://3vee.molmovdb.org.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Internet
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Conformation*
  • RNA / chemistry*
  • Software*
  • User-Computer Interface


  • RNA