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.
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Michel Petitjean (1995) studied this question.
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