Tunnels and Voids in Molecules via Voronoi Diagram

Abstract

Molecular external structure is important in understanding molecular interaction with its solvent environment and is useful in developing drugs. Important examples of external structures are tunnels, pockets, caves, clefts, voids, etc. This paper presents an algorithm to extract tunnels and voids from molecular structures. The algorithm is based on the the Voronoi diagram of atoms in molecules and its time complexity is $O(m)$ time in the worst case, where $m$ represents the number of entities in the Voronoi diagram.