Three-Dimensional Similarity Based on Steric Properties

Three-Dimensional Similarity Based on Steric Properties 

Doweyko reported on a similar program that runs on a personal computer. In this case, 2.8-4.0 A spacings are used and occupancy and a crude description of electronegativity are recorded. The fit of a test molecule to the 

D-2 dopamine receptor. The statistical models are cross-validated and have been shown to have good predictive utility. In this scheme, two molecules would be similar in three-dimensional properties if they are similar in those three-dimensional properties associated with the biological property of interest. 

Dean and Chau have used this method to measure the similarity of the accessible and molecular electrostatic potential surfaces of two marine neurotoxins. One superposition used the rms value of eight atoms.In this orientation, the electrostatic potential surfaces were found to have a rank correlation coefficient of approximately 0.8. In a different superposition, the surfaces were compared to determine orientations that give maximal correspondence of the surface property. Here, several superimpositions, illuminating the relatively high degree of similarity between the accessible surfaces of these dissimilar molecules, were found. 

It can be seen that the definition of three-dimensional similarity is not a solved problem but rather an area of active research. It is possible that the most appropriate definition will depend on the structures of the molecules investigated and on the property to be compared. Thus, computer programs that perform three-dimensional searches might need to include a variety of definitions of similarity. 

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