ORGLIST: What is a structural representation in chemistry?

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From: z17b3 (z17b3$##$unb.ca)
Date: Mon Feb 05 2001 - 21:16:21 EST


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 (postscript-version)
http://www.cs.unb.ca/profs/goldfarb/cadd.pdf (pdf-version)

(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$##$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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