Maximal common substructure, MCS

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. 

The final measure of similarity that we have used is the maximal common substructure (MCS), i.e., the largest pattern of atoms in 3-D space that are identical in the two molecules that are being compared. If the MCS contains MCSiAyB) atoms, then the similarity between A and B is defined to be... 

Three main types of similarity measure have been used for quantifying the degree of resemblance between pairs of 2D chemical structures, these measures being based upon fragment substructures, topological indices, or maximal common subgraph (MCS) isomorphism algorithms. 

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