Protocols

VLDP specifications

Information


Unique identifier OMICS_10018
Name VLDP
Alternative name Voronoi Laguerre Delaunay Protein
Interface Web user interface
Restrictions to use None
Input data A PDB file and chain IDs
Output data VLDP provides output in two complementary forms: direct visualization of the Laguerre tessellation, mostly its polygonal molecular surfaces, files of volumes, and areas, contacts and similar data for each residue and each atom. These files are available for download for further analysis.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jérémy Esque

Publication for Voronoi Laguerre Delaunay Protein

VLDP citations

 (2)
library_books

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

2016
PLoS One
PMCID: 4704809
PMID: 26741367
DOI: 10.1371/journal.pone.0145848

[…] h closer optimum activity temperatures.To verify our findings we evaluate our entire dataset with an alternative method used to measure the quality of atomic packing in protein structures. We use the VLDP web server (http://www.dsimb.inserm.fr/dsimb_tools/vldp/) to compute residue contact number for each residue cluster. VLDP uses a Laguerre Tessellation to evaluate residue volumes in protein stru […]

call_split

Structural neighboring property for identifying protein protein binding sites

2015
BMC Syst Biol
PMCID: 4565107
PMID: 26356630
DOI: 10.1186/1752-0509-9-S5-S3
call_split See protocol

[…] We use VLDP [] for geometrically analyzing protein 3D structures, based on Voronoi Tessellation. Voronoi Tessellation is a partition of space into polyhedra, whereas Delaunay diagram builds a graph with vert […]

VLDP institution(s)
LPTM, CNRS UMR 8089, Université Cergy-Pontoise, Cergy-Pontoise, France

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