Voronoia -- Voronoi Cell Protein Packing Database
What you can do:
Analyze and visualize the atomic packing of protein structures.
Highlights:
- Voronoia is a database of atomic-scale packing data for protein 3D structures.
- It is based on an improved Voronoi Cell algorithm using hyperboloid interfaces to construct atomic volumes, and to resolve solvent-accessible and -inaccessible regions of atoms.
- The database contains atomic volumes, local packing densities and interior cavities calculated for 61,318 biological units from the PDB.
- A report for each structure summarizes the packing by residue and atom types, and lists the environment of interior cavities.
- The packing data are compared to a nonredundant set of structures from SCOP superfamilies.
- Both packing densities and cavities can be visualized in the 3D structures by the Jmol plugin.
- PDB files can be submitted to the Voronoia server for calculation.
- This service performs calculations for most full-atomic protein structures within a few minutes.
Keywords:
- protein packing
- Voronoi cell algorithm
- packing densities
- ligands
Literature & Tutorials:
PubMed Link: Voronoia: analyzing packing in protein structures
This record last updated: 04-21-2014