Voronoia protocols

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Voronoia specifications

Information


Unique identifier OMICS_07912
Name Voronoia
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Kristian Rother <>

Information


Unique identifier OMICS_07912
Name Voronoia
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kristian Rother <>

Publication for Voronoia

Voronoia in pipeline

2016
PMCID: 4846865
PMID: 27118724
DOI: 10.1038/srep25070

[…] tripeptides, were calculated with accelrys discovery studio using a using 1.4 å radius probe and 240 grid points per atom. atomic packing densities were calculated from voronoi volumes using the voronoia webserver (http://bioinformatics.charite.de/voronoia). multiple linear regression was performed with origin 9, fitting to rmsf = a(relative sasa) +b(b-factor) +c. images were rendered […]


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Voronoia in publications

 (4)
PMCID: 3493521
PMID: 23145167
DOI: 10.1371/journal.pone.0049375

[…] between residues in the respective c-terminal segments, interacting in a parallel fashion. this led to dodecamers that appeared to be packed well. the packing densities were measured using voronoia . all models had average values of 0.8, which is identical to the tetramer aβ (17–42) crystal structure., all initial models consist of a hydrophobic inner core formed by c-terminal […]

PMCID: 3392262
PMID: 22808083
DOI: 10.1371/journal.pone.0039993

[…] average packing density of proteins is about 0.75. comparative studies of packing density and cavity analysis of similar nmr and crystal structures for all classes of proteins was performed using voronoia . the grid level for all the input pdbs were adjusted to 0.2 for calculating the parameters. this analysis, however, did not yield new information, apart from confirming that nmr structures […]

PMCID: 3312204
PMID: 22451863
DOI: 10.1038/srep00334

[…] is computed using naccess. both absolute accessible surface area (asa) and relative surface accessibility (rsa) have been computed. the local packing density for each residue is calculated using voronoia program suite. it employs voronoi tessellation to assess the spatial proximity of atoms in 3dspace. the packing density for an atom was computed as the fraction of the voronoi polyhedron […]

PMCID: 3123238
PMID: 21605466
DOI: 10.1186/1471-2105-12-195

[…] be its voronoi volume [,] (which is the volume of a polyhedron, systematically extended around the atomic group until it comes into contact with similar polyhedra in its neighborhood). the program voronoia.exe [,] was used to compute local packing densities around residues within a polypeptide chain. in this software, instead of voronoi volume, solvent excluded (se) volume [] of the atomic […]


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Voronoia institution(s)
Institute of Molecular Biology and Bioinformatics, Charité - University Medicine Berlin, Berlin, Germany

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