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 alpha and beta, where alpha is the radius of the solvent molecule (also known as the probe-radius) and beta 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(n k \log^2{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 alpha and beta.