Molecular similarity/diversity

A powerful extension to the potential pharmacophore method has been developed, in which one of the points is forced to contain a special pharmacophore feature, as illustrated in figure 4. All the potential pharmacophores in the pharmacophore key must contain this feature, thus making it possible to reference the pharmacophoric shapes of the molecule relative to the special feature. This gives an internally referenced or relative measure of molecular similarity/diversity. The special feature can be assigned to any atom-type or site-point, or to special dummy atoms, such as those added as centroids of privileged substructures [7, 10]. With one of the points being reserved for this special feature, it would seem even more necessary to use the 4-point definition to capture enough of the... 

A special case of cell-based methods is a diversity measure proposed for binary fingerprints. Unlike continuous descriptors, binary descriptors such as structural keys and hashed fingerprints can be compared using fast binary operations to give rapid estimates of molecular similarity, diversity, and complementarity. The most common example of a diversity measure applied to binary descriptors is the binary union (inclusive or ). This can be exploited in a number of different ways elegant examples can be found in the following references. ... 

Godden, J.W., Xue, L. and Bajorath, J. (2000). Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations Using Binary Fingerprints and Tanimoto Coefficients. J.Chem. lnf.Comput.Sci., 40,126-134. 

Godden JW, Xue L, Bajorath J. Combinatorial preferences affect molecular similarity/ diversity calculations using binary fingerprints and Tanimoto coefficients. J Chem Inf Comput Sci 2000 40 163-166. 

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