3V: cavity, channel and cleft volume calculator and extractor
By Neil Voss, Mark Gerstein. Nucleic Acids Res., 2010
474 citations recorded by the source corpus.
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 Å 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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/014aaec1afa70d8cb71b769f67f8797ff6dea610
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In Molecular Biology
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Citations in the corpus
- Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016, background): “The recently developed, well-documented 3V web interface for volume, solvent exclusion and channel prediction does not compute SASA values per residue [24].”
- MOLE 2.0: advanced approach for analysis of biomacromolecular channels (2013, methodology): “These methods are used in numerous software tools, such as POCKET [24], LIGSITE [25,26], dxTuber [27], HOLLOW [28], 3V [29], CAVER 1.”
- Structural basis of WLS/Evi-mediated Wnt transport and secretion (2020, methodology): “Model analysis—A cavity search using the Solvent Extractor from Voss Volume Voxelator server (Voss and Gerstein, 2010) was performed using an outer-probe radius of 15 Angstrom and inner-probe radius of 2 Angstrom.”
- CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures (2012, background): “Recently, several geometry-based tools for rapid identification and analysis of pathways in protein structures have been developed [35–44].”