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Number of citations per year for the bioinformatics software tool 3V
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Protocols

3V specifications

Information


Unique identifier OMICS_04694
Name 3V
Alternative name Voss Volume Voxelator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Neil R. Voss

Information


Unique identifier OMICS_04694
Name 3V
Alternative name Voss Volume Voxelator
Interface Web user interface
Restrictions to use None
Output data The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Neil R. Voss

Publication for Voss Volume Voxelator

3V citations

 (5)
library_books

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta Lactamases

2016
PLoS Comput Biol
PMCID: 4917113
PMID: 27332861
DOI: 10.1371/journal.pcbi.1004926

[…] Residues that are exposed to the active site cleft were identified using a method employing the Voss Volume Voxelator (3V) []. The Solvent.exe program in the 3V distribution was executed using a grid spacing of 0.5Å, a small probe radius of 1.5Å and a big probe radius of 6Å. Residues in position […]

library_books

AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1 Proteinase Inhibitor

2016
PLoS One
PMCID: 4805282
PMID: 27008547
DOI: 10.1371/journal.pone.0151902

[…] the Standard Voronoi procedure where the Shrake method was applied to calculate Van der Waals radii and to assess the solvent accessible surface area. Additionally, the volume was calculated with 3V (Voss Volume Voxelator: http://3vee.molmovdb.org) volume assessor by rolling a virtual probe over the 1qlp protein surface [,]. The probe radius of 1.4, 3 and 10 Å was applied to obtain the solvent-exc […]

library_books

Cytochrome P450 125A4, the Third Cholesterol C 26 Hydroxylase from Mycobacterium smegmatis

2015
Biochemistry
PMCID: 4660985
PMID: 26522442
DOI: 10.1021/acs.biochem.5b01029

[…] W. This change allows the 7α-hydroxycholesterol ligand greater access to the active site in the mutant than in the wild-type enzyme. Using the discrete volume determination method employed by 3V, the Voss Volume Voxelator, and with the probe radius set to 1.5 Å, the channel volume in the CYP125A3 W83Y structure is found to be enlarged versus that of the wild-type CYP125A3 structure by 32 Å3, 22 Å3 […]

call_split

Structure and properties of the esterase from non LTR retrotransposons suggest a role for lipids in retrotransposition

2013
Nucleic Acids Res
PMCID: 3905857
PMID: 24003030
DOI: 10.1093/nar/gkt786
call_split See protocol

[…] (ZfES_BA, connecting residues M135-L199 from chain B with residues R200-I302 from chain A) was also achieved in COOT followed by energy minimization in PHENIX. Cavity volumes were extracted using the Voss Volume Voxelator () using inner and outer probe radii of 1.2 and 5.0 Å, respectively. Figures were generated in PyMOL (http://pymol.org/) using the APBS plug-in () to visualize electrostatic surf […]

call_split

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein Protein Complexes in the Cell

2010
PLoS One
PMCID: 2887369
PMID: 20567518
DOI: 10.1371/journal.pone.0011169
call_split See protocol

[…] Structures were prepared for calculation using PDB2PQR software (version 1.3) . The volume of interacting partners (vol) was calculated using 3v: Voss Volume Voxelator (version 1.2) , solvent-accessible surface area (SASA) using DSSP , while hydration free energy (HFE), electrostatic energy (EE) and radius of gyration (Rgyr) were calculated usi […]


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3V institution(s)
Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA

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