Similarity searching maximal common substructure

The subsimilarity search method developed at the Upjohn Company, which is discussed later, measures the similarity between a pair of molecules by the maximal common substructure (MCS), that is, the largest substructure that is common to the two molecules that are being compared, as illustrated in Figure 4. The system utilizes an inverse-frequency weighting scheme that favors heteroatom-heteroatom pairs over the mote frequently occurring carbon-carbon pairs. For each pair of heteroatoms separated by minimum paths of two to six bonds, an additional bond is added to link the atoms directly. This additional link results in an increase in the size of the MCS and thus a greater similarity for heteroatom-containing common substructures. 

Similarity searches have been applied to the interpretation of H and C NMR spectra and IR spectra. In one approach, a C NMR similarity search, using the spectrum of an unknown as the query, is followed by application of a maximal common substructure algorithm to identify the most common substructures in the set of structures corresponding to the retrieved spectra, If known, the molecular formula of the query can be used to reduce the number of retrieved structures prior to the latter step. The study demonstrated that the substructures predicted in this fashion usually reveal important structural features of the unknown, which can be used directly as constraints in structure generation. 

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