What Is a Structural Representation in Chemistry: Towards a Unified Framework for CADD?

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A fundamentally new formal framework for structural representation of organic compounds based on the first "true" (general) formalism for structural object representation recently proposed by us|evolving transformation system (ETS) model is outlined. The applied orientation of the paper is towards the molecular design in general and computer aided drug design (CADD) in particular. Inadequacies of the conventional models used in (CADD) for molecular representation and classification as well as the advantages of the proposed ETS model are discussed. Some advantages of the ETS model is its capability to represent naturally all important structural features of molecules, e.g. different atoms and their bonding types (including hydrogen bonding), basic 2D and 3D isometries, the molecular class structure. The model allows one not only to classify a new compound, but also to construct a chemically valid new compound from the class of compounds that was previously learned based on a small set of examples. The model also guarantees the inheritance of the chemical structural class information from the parent class to all its subclasses. In general, the ETS model offers a much more precise "language" for chemical structural formulas. The central role of the class learning problem in CADD is suggested. Moreover, we propose the ETS model as a unified framework for the class learning problem and therefore as a unified formal framework for CADD. This would allow considerable streamlining of the CADD by assigning to the chemist the role of an interactive user of the system rather that a role of a human weak link within the CADD process.