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Dear colleagues, The following paper that proposes some revolutionary ideas related to the nature of structural representation in chemistry might be (either directly or indirectly) of interest to you: http://www.cs.unb.ca/profs/goldfarb/cadd.ps (the abstract is appended below). Please note that although the applied focus of the paper is the area of computer aided drug design, ANY other area of theoretical or applied chemistry could have been chosen instead. Best regards, Lev Goldfarb Tel: 506-458-7271 Faculty of Computer Science Tel(secret.): 453-4566 University of New Brunswick Fax: 506-453-3566 P.O. Box 4400 E-mail: [log in to unmask] Fredericton, N.B., E3B 5A3 Home tel: 506-455-4323 Canada http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm ****************************************************************************** * WHAT IS A STRUCTURAL REPRESENTATION IN CHEMISTRY: TOWARDS A UNIFIED FRAMEWORK FOR CADD? Lev Goldfarb, Oleg Golubitsky, Dmitry Korkin Faculty of Computer Science University of New Brunswick, P.O Box 4400 Fredericton, N.B., Canada ABSTRACT. A fundamentally new (and, we believe, the first) model for structural representation of molecules, with general emphasis on drug design applications, is outlined. This is the first formal model that was motivated by the structural description of classes. The model, in particular, guarantees the inheritance of the chemical structural class information from the parent class to all its subclasses. Inadequacies of the conventional models used in computer aided drug design (CADD) for molecular representation and classification as well as the advantages of the proposed--evolving transformation system (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 compound, but also to construct a chemically valid compound from the class of compounds that was previously learned. Hence, in particular, the 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.