Geometric molecular similarity from volume-based distance minimization: Application to saxitoxin and tetrodotoxin

The geometric molecular dissimilarity between two molecules is defined as the difference between the volume of their union minus the volume of their intersection. This dissimilarity has the mathematical properties of a distance. This distance is minimized under all rotations and translations using a discrete Broyden, Fletcher, Goldfarb & Shanno (B.F.G.S.) algorithm. The optimal geometric superimposition of saxitoxin and tetrodotoxin is discussed. © 1995 by John Wiley & Sons, Inc.