PrinCCes

PrinCCes decomposes internal void volumes in proteins and protein complexes into distinct continuous voids and produces triangulated surface representations to analyze the spatial configuration and accessibility of grooves, pockets, channels, chambers, cavities, and tunnels.

Key Features:

• Void decomposition algorithm: Decomposes the entire void volume into distinct entities based on spatial continuity and defines continuous voids by the ability of a spherical probe to move freely between any two internal points.
• Complex topology handling: Detects continuous voids regardless of topological complexity, accommodating structures with multiple holes and bifurcations.
• Triangulated surface visualization: Produces triangulated surface representations of individual voids or combinations of voids for spatial analysis.
• Export to molecular viewers: Outputs compatible with VMD (Visual Molecular Dynamics) and Chimera for 3D rotation and image generation.

Scientific Applications:

• Drug Design and Discovery: Visualizes binding sites and channels to support identification of potential drug targets and optimization of ligand interactions.
• Protein Engineering: Characterizes internal void geometry to inform design of proteins with modified properties or functions.
• Structural Biology Research: Enables detailed analysis of protein voids to support insights into structural mechanisms and accessibility.

Methodology:

Decomposes void volume based on spatial continuity using a spherical-probe accessibility criterion, generates triangulated surface representations of voids, and exports results compatible with VMD and Chimera.