Nucleic Acids Research · 2010 · 490 citations · 32 references
Life SciencesBioinformaticsBiophysicsStructural BioinformaticsStructural BiologyStructural BiophysicsBiomolecular StructureExcluded Volume ModelingMacromolecular Structure DeterminationNucleic Acid ModelingProtein StructureRna StructureExcluded Volume FeaturesExcluded Volume MappingMacromolecular Structure VisualizationMolecular VolumeNucleic Acid Structure DeterminationRna Structure DeterminationSolvent Excluded SurfaceWeb Server Architecture
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.
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Helen M. Berman · Nucleic Acids Research · 2000 · 39.8K citations
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
Nenad Ban, Poul Nissen, J.L. Hansen et al. · Science · 2000 · 3.3K citations