3V statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Channel detection Volume calculation Tunnel detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

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 in publications

 (5)
PMCID: 4917113
PMID: 27332861
DOI: 10.1371/journal.pcbi.1004926

[…] of the initial assp and its processing to produce the final assp is described in figs and ., 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 3905857
PMID: 24003030
DOI: 10.1093/nar/gkt786

[…] 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 […]

PMCID: 2887369
PMID: 20567518
DOI: 10.1371/journal.pone.0011169

[…] the characteristics of their interacting partner., 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

3V reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review 3V