A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

A Gaussian description of molecular shape is used to compare the shapes of two molecules by analytically optimizing their volume intersection. The method is applied to predict the relative orientation of ligand series binding to the proteins, thrombin, HIV protease, and thermolysin. The method is also used to quantify the degree of chirality of asymmetric molecules and to investigate the chirality of biphenyl and the amino acids. The shape comparison method uses the newly described shape multipoles that can also be used to describe the inherent shape of molecules. Some results of calculated shape quadrupoles are given for the ligands used in this work.