Compound maximum common substructure

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). 

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. 

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

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. 

Varmuza K, Penchev PN, Scsibrany H. Maximum common substructures of organic compounds exhibiting similar infrared spectra. J Chem Inf Comput Sci 1998 38 420-427. 

There are four methods for 3D data base searching distance distributions, individual distances, maximum common substructure, and atom mapping in her book, Catherine Pepperrell emphasizes the latter method, and also addresses dissimilarity (which matters when searching for new lead compounds, and one wishes to screen as many different classes as possible). 

In general, the term scaffold is applied in a multimde of ways to describe a molecular core structure, for example, as a common element of a chemical series or for building blocks in synthetic chemistry. For closely related compounds, such a scaffold could be defined by their maximum common substructure (MCS) [22]. 

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