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