Voronoia

Voronoia calculates atomic packing density in macromolecular structures using the Voronoi cell method to quantify free space between neighboring atoms, assess van der Waals interactions, and identify packing defects.

Key Features:

• Automated atomic packing density computation: Performs automated calculations of atomic packing density for macromolecular structures using the Voronoi cell method.
• Voronoi-based free-space estimation: Quantifies free space between neighboring atoms by explicitly computing Voronoi cells to detect volume and packing defects.
• Precomputed PDB database: Provides an updated collection of precomputed packing densities for entries from the Protein Data Bank (PDB).
• Filtering options: Supports filters to refine searches and analyses of packing density results and computed voids.
• Applicability to proteins and RNA: Targets structural analyses of proteins and RNA to evaluate packing, voids, and related interactions.

Scientific Applications:

• Functional analysis of 3D structures: Relates atomic packing density and internal voids to functional features in proteins and RNA.
• Structural model quality assessment: Identifies regions with large internal voids that may indicate model inaccuracies or areas needing refinement.
• Detection of unresolved waters and ions: Locates internal voids that can suggest unresolved water molecules or ions in structural models.
• Identification of cryptic ligand binding pockets: Detects internal cavities that may represent cryptic or hidden ligand binding sites.
• Support for molecular simulations: Provides packing-density information relevant to the setup and validation of molecular simulations involving proteins and nucleic acids.

Methodology:

The methodology uses the Voronoi cell method to estimate free space between neighboring atoms, thereby assessing van der Waals interactions and identifying packing defects.