Defining, computing, and visualizing molecular interfaces

A parallel, analytic approach for defining and computing the inter and intra molecular interfaces in three dimensions is described. The molecular interface surfaces are derived from approximations to the power diagrams over the participating molecular units. For a given molecular interface our approach can generate a family of interface surfaces parametrized by α and β, where α is the radius of the solvent molecule (also known as the probe radius) and β is the interface radius that defines the size of the molecular interface. Molecular interface surfaces provide biochemists with a powerful tool to study surface complementarity and to efficiently characterize the interactions during a protein substrate docking. The complexity of our algorithm for molecular environments is O(nk log² k), where n is the number of atoms in the participating molecular units and k is the average number of neighboring atoms-a constant, given α and β