Squares, molecular structural motifs

In our molecular overlay approach, optimized geometries of the two structures to be compared are overlaid, and the root mean square distance (RMSD) between the atoms is considered as the measiue of similarity between the two overlaid structures. Two or more structures can be overlaid with respect to the atoms specified by the user, and the RMSD can be measiued for any user-defined set of atoms, backbone atoms or aU of the atoms including hydrogen. Due to this advantage, the approach could be used to overlay even structurally dissimilar molecules, as long as they have a common motif. One can zero in on a putative pharmacophore/biophore by overlaying... 

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