Subject: Re: pattern recognition and databases

From: Suzanne Sirois <[email-masked]>
Date: Thu, 8 Jul 1999 15:05:45 -0400 (EDT)

Dear CClers,
 I wish to extend my thanks to those people who replied to my question.

In response to my question:
"on the application of Neural Networks or Genetic
algorithms or any statistical methods for the discovery
of patterns in databases."

First, lets mention that there is basically three different approaches 
for 3D database searching and they are a direct consequence of the 
fact that the principles that govern ligand-receptor interaction
recognition still remain unclear.

1)I.D. Kuntz focusses on the protein-structure-driven shape matching aspects

2)Y.C. Martin focusses on the medicinal perspective (i.e. pharmacophore) 

3)P. Willet focusses on the algorithm and information retrieval aspects.

You will find a comparison of the three techniques at the URL:
htpp://www.netsci.org/Science/Cheimform/feature06.html
This reference is not concern
with the application on NN or GA to database mining but raises the important 
point that good ideas translate eventually into good queries.

Amongst many references, 
one very comprehensive article on similarity searching using GA 
can be found at the URL:
http://www.ijc.com/articles/1998v1/37/
The authors use a 
Genetic Algorithm to align molecules in a large 3D
database and assess the relationship between their
similarity and biological activity.  (Nick Jewell)
It will be interesting to know if this approach has been apply 
with DFT-derived MEP and electron density. 

A very important link containing a list of Evolutionary Algorithms 
in Computer-Aided Molecular Design can be found at the URL:
http://panizzi.shef.ac.uk/cisrg/links/ea_bib.html
and is maintained by David E. Clark.

In conclusion, it seems nowadays that one of the most important 
challenging problem in CADD, CAMD is the scoring function and 
it is a direct consequence of our understanding of the 
ligand-receptor interaction. If it is beyond our actual perception and 
understanding will it be possible to develop and apply
searching method such as GAs that will guide us in the comprehension
analysis and treatment of very complex system (i.e. discovery of
patterns in database for the formulation of novel ideas and 
better queries.)

Kind Regards,

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*  Suzanne Sirois Ph.D.                         *
*  Computational (bio) chemistry                *
*                                               *
*  Office  CERCA/Alliance Pharma                *
*  (Centre de Recherche en Calcul Applique)     *
*                                               *
*  e-mail: [email-masked]           *
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