Markush structure handling

Most of the descriptors discussed in this review require an enumerated structure, i,e., the full connection table of the reference molecule. For combinatorial libraries and for certain kinds of descriptors, this is not necessary. Downs and Barnard have recently presented an elegant method to compute molecular fingerprints based on the precursors, using techniques developed for Markush structure handling in chemical patents,... 

Enumerating the product space of combinatorial libraries and calculating the descriptors can be expensive computationally. Recently, Downs and Barnard [62] have described an efficient method of generating fingerprint descriptors of the molecules in a combinatorial library without the need for enumeration of the products. This method is based on earlier technology for handling Markush structures. An alternative approach is to use random sampling techniques to derive a statistical model of the property under consideration [63],... 

W. Fisanick, Requirements for a System for Storage and Search of Markush Structures in Computer Handling of Generic Chemical Structures , eds. J. M. Barnard, Gower, Aldershot, UK, 1984, pp. 106-129. 

The problem of poor retrieval precision, and the development of search systems based on unambiguous (complete) representations of the structure has led to the general demise of fragment codes as a primary representation of chemical structures, at least for specific compounds. However, hidden from the user they remain an important component of structure search systems, and a few user-visible fragment-code systems continue to be used in the handling of Markush structures from chenaical patents these are discussed in more detail in Markush Structure Searching in Patents. 

A number of special methods for handling synthetic polymers have been developed. These can generally be divided into those that are based on representations of the monomer precursor(s), and those based on the structural repeating units (SRUs) of the polymer itself. The former obviously requires little extension to the system for small molecules, except the inclusion of some indication that the representation is of a polymer of... the structure shown. There are some similarities in the requirements for SRU-based representations and those for handling Markush structures, especially where copolymers are concerned. 

The concept of superatoms included in the SMD format permits a structured representation of (large) molecules and reactions. Furthermore we believe that this concept indicates a possible way of handling generic structures and Markush formulas. We do not have a final solution for these problems yet, but promising attempts are under investigation. 

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