Voronoia

Voronoia is a software tool that enables automated analysis of the atomic packing density in macromolecular structures, such as proteins and RNA. It combines previous efforts into a single service with advanced online visualization. Using the Voronoi cell method, Voronoia calculates the free space between neighboring atoms to estimate van der Waals interactions and explicitly considers volume or packing defects. Large internal voids identified by Voronoia can indicate unresolved water molecules, ions, cryptic ligand binding pockets, or parts of the structural model requiring further refinement. The tool is primarily used for functional analyses of 3D structures and quality assessments of structural models. The updated version, Voronoia 4-ever, includes a database of precomputed packing densities for PDB entries, allows uploading multiple structures, adds new filter options, and provides intuitive results display using the NGL viewer.