Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms.