Effect of standardization on fragment-based measures of structural similarity

Substructural fragment occurrence data are widely used as the basis for measures of inter-molecular structural similarity. This paper investigates the effect of standardization on the effectiveness of such measures using eight data sets for which both structural and biological activity data are available. Eight different standardization methods are studied and it is shown that there is no significant difference in the effectivenesses of the various methods; accordingly, any of them can be used for the calculation of intermolecular structural similarity.