Maximum common substructure

A key concept in the assessment of molecular similarity based on chemical graphs is that of a maximum common substructure, MCS(G,GJ), of two chem-... 

Fig. 1. An example of two hydrogen-suppressed graphs G1 G2 and a common substructure CSIG,, G2) and the maximum common substructure MCS(G1 G2) are shown above. The Tanimoto similarity index and the distance between the two chemical graphs are computed below.

Cuissart, B., Touffet, F., Cremilleux, B., Bureau, R., and Rault, S. (2002) The maximum common substructure as a molecular depiction in a supervised classification context experiments in quantitative structure/biodegradability relationships. J. Chem. Inf. Comput. Sci. 42, 1043-1052. 

Figure 8.5 Maximum Common Substructure of two molecules (MCS, drawn in bold). The structure on the left is the example structure from Figure 8.1. The structure on the right is vanillyl-N-nonylamide, IUPAC name N-[(4-hydroxy-3-methoxy-phenyl)methyl]nonanamide, PubChem CID 2998.

Fragment- or substructure-based descriptors include maximum common substructures (MSC) or combinations of scaffolds or subscaffolds. Simple numeric descriptors include calculated LogP,... 

Stahl, M. and Mauser, H. 2005. Database clustering with a combination of fingerprint and maximum common substructure methods. J. Chem. Inf. Model. 45, 542-548. 

It is often possible to draw multiple generic structures for a combinatorial library. Care should be taken in the choice of the appropriate structure, taking into account the purpose for the structure. Often the maximum common substructure is a good choice, but other structures may better illustrate structure-activity relationships or the synthetic potential of a combinatorial reaction strategy. The relationship between residue and reagent or product should be defined. This may be conveniently shown in the generic reaction scheme see Figure 12A-1. 

A tremendous number of various fragments are used in structure-property studies atoms, bonds, topological torsions , chains, cycles, atom- and bond-centered fragments, maximum common substructures, line notation (WLN and SMILES) fragments, atom pairs and topological multiplets, substituents and molecular frameworks, basic subgraphs, etc. Their detailed description is given below. 

The focus is the - maximum common substructure among the experimental compounds corresponding to a molecule with a measured response, i.e. it is the parent molecule. 

The MCS is a measure and a description of the similarity of two structures whose numerical value MCS is the number of common elements provided by the matching conditions, i.e. a measure of the size of the maximum common substructure. It is commonly used in -> similarity searching [Scsibrany and Varmuza, 1992b]. 

A measure of similarity obtained by the maximum common substructure between two compounds s and t is given by ... 

Scsibrany, H. and Varmuza, K. (1992b). Topological Similarity of Molecules Based on Maximum Common Substructures. In Software Development in Chemistry - Proceedings of the 7th CIC-Workshop Computers in Chemistry" (Ziessow, D., ed.), Berlin/Gosen (Germany). 

Varmuza, K., Penchev, P.N. and Scsibrany, H. (1998). Maximum Common Substructures of Organic Compounds Exhibiting Similar Infrared Spectra. J.Chem.lnf.Comput.ScL, 38, 420-427. 

A reference compound (or reference stmcture) is a compound assumed as the reference for some considered aspect, such as a physico-chemical or biological property, or a molecular skeleton common to a set of compounds ( maximum common substructure). 

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