What is a structural representation in chemistry?

Dmitry Korkin z17b3 at unb.ca
Sun Feb 4 23:02:41 EST 2001

    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:


 (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: goldfarb at unb.ca    
Fredericton, N.B., E3B 5A3                     Home tel: 506-455-4323        
Canada        http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm


                    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.


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