Subject: summary of AI and NN groups

From: [email-masked] (Douglas A. Smith Ph.D.)
Date: Fri, 25 Oct 1996 12:16:29 -0400

On 17 October, I asked:

"I am interested in finding out what academic research groups are involved in
developing and using artificial intelligence, neural networks, genetic
algorithms, etc. for QSAR and QSPR, for molecular modeling and property
prediction, etc. Please respond directly to me; I will summarize if there is
sufficient interest.I am interested in finding out what academic research
groups are involved in developing and using artificial intelligence, neural
networks, genetic
algorithms, etc.for QSAR and QSPR, for molecular modeling and property
prediction, etc. Please respond directly to me; I will summarize if there is
sufficient interest."

The edited summary of responses follows.  Several responses either from or
describing industrial/commercial work are also included.  Thanks to all who
answered.

Doug

============================================================================
===========

        The two QSAR/QSPR groups that I know of are A Hopfinger at the
University of Illinois at Chicago &  P. Jurs at Penn State.  Both of these
groups have done research in the GA and NN areas.  They each have their own
little niches though.  If you would like some more info. on these groups,
feel free to contact me -- I am quite familiar with the work from both
groups.  
 
 Ray Crawford
 Research Associate
 Procter & Gamble

============================================================================
===========

We are as you probably know. See our papers at 1st electronic conference 
of Molecular Graphics society,

http://bellatrix.pcl.ox.ac.uk/mgms/

I'll be happy to provide additional information.

Alexander Tropsha, Ph.D.              
Assistant Professor, Director the Laboratory for Molecular Modeling 
School of Pharmacy                    
University of North Carolina          

============================================================================
============

I know that the department of analytical chemistry of my university
applies some research in AI,NN and Gentetic algorithm, for e.g. 
property prediction.

Their WWW-address is : http://www-cac.sci.kun.nl/cac/index-nl.html

Unfortunately their home page is in dutch, however the rest is in 
english. So I should say look at the links research, projects, LAC 
verwijzingen and recente publicaties.

Niels J. van der Laag 
Dept. of Physical Chemistry
University of Nijmegen 

============================================================================
===========

maybe you are interested in this URL:

http://www.tu-bs.de/institute/org-chem/herges/akherges.html

J.Grunenberg, Organische Chemie, Hagenring 30, 38106 Braunschweig de

============================================================================
===========

I have done a fair bit with neural nets in an academic sense (chance 
effects, overfitting, overtraining, pruning methods) and also apply 
them (when appropriate) to QSAR/QSPR problems.  I can let you have 
references to papers and book chapters if you are interested.

D.J. Livingstone 
ChemQuest

============================================================================
===========

We are doing nn analysis of clinical databases for database mining, disease
stratification and disease process modeling using petri nets and stochastic
activity nets, hypothesis evaluation against large databases, oodb
development for gene discovery against clinical data, etc.

Michael N. Liebman, Ph. D.
Director, Bioinformatics and Genomics
Vysis, Inc.

============================================================================
===========

Prof. J. Gasteiger's group at Computer-Chemistry-Center, Erlangen, Germany
is one of such a research group. Please check

http://www.ccc.uni-erlangen.de/

Lingran Chen, Ph.D.
Chemistry Department
Brandeis University

============================================================================
===========

I do a fair bit of this work for drug and crop protection agents design at
CSIRO.  I'm also collaborating with Prof. Frank Burden in the chemistry
department, Monash University.  We use NN and GAs for a number of problems
in drug design, environmental and forensic chemistry.

Vladimir Brusic at the Walter and Eliza Hall Institute for Medical research
in Melbourne is also using NN to carry our QSAR in peptide ligands.  Des
Maddalena in the pharmacolgy department, University of Sydney is using NN
in QSAR and clinical medicine.

The groups overseas I'm involved with are run by Gerry Maggiora at Upjohn,
Yoshi Takahashi at the Toyohashi University of Technology and Tariq Andrea
at Du Pont's Stine Haskell Labs.

Dr. David A. Winkler                             
Principal Research Scientist                     
CSIRO Division of Chemicals and Polymers         h
ttp://www.csiro.au

============================================================================
===========

Send a message to Daniel Vercauteren in Namur, Belgium:

[email-masked]

Guy Baudoux
University of Namur, Belgium

============================================================================
===========

We use genetic algorithms quite a lot in our group here at Sheffield
University, for a number of problems related to molecular similarity,
protein structure prediction, diversity analysis, etc. A list of the
projects is on our web site
(www.shef.ac.uk/uni/academic/I-M/is/research/cisrg/chem.html). I use a GA
for aligning electrostatic, hydrophobic and shape fields around molecules,
both for QSAR and so that similarity can be calculated between them, for
database similarity searching.

Dr. David Wild, Department of Information Studies,
University of Sheffield, Sheffield S10 2TN, U.K.

============================================================================
===========

I am working in Sheffield University, in collaboration with Glaxo
Wellcome and the CCDC, on developing a genetic algorithm for flexible
ligand docking.  The software has recently been tested on 100
protein-ligand complexes extracted from the PDB.

I've also developed a related program that superimposes small flexible
molecules in order to automatically elucidate pharmacophores.  This
program, called GASP, is now available from Tripos Inc.

If you want to know more you might want to look at these web pages.
http://panizzi.shef.ac.uk/gareth/

Dr Gareth Jones
Dept of Information Studies and Krebs Institute for Biomolecular Research
University of Sheffield, UK

============================================================================
===========

Our research group at Moscow State University is involved in developing 
and using neural networks for QSAR and QSPR. We have developed in-house
program NASA (Neural Approach to Structure-Activity) for Windows for
this purpose.

Some on-line abstracts of our papers:
http://org.chem.msu.su/people/baskin/articles/ref040ab.html
http://org.chem.msu.su/people/baskin/articles/ref043ab.html
http://org.chem.msu.su/people/baskin/articles/ref069ft.html

Dr. Igor I. Baskin
Dr. Vladimir A. Palyulin

============================================================================
===========

The Institute for Tumor Biology-Cancer Research and the Austrian
Research Institute for Artificial Intelligence will start a project next
year. It contains the development and application of Inductive Logic
Programming (ILP) methods to learn SARs for noncongeneric
(carcinogenicity) databases. We will use several new approaches to
include detailed biological data (species, sex and organ specific
effects) and to optimize the choice of chemical descriptors. Please
contact me, if you need further details.

Christoph Helma	 <[email-masked]>			
Inst. f. Tumorbiologie- Krebsforschung

============================================================================
===========

You might contact Bill Dunn at U of I, Chicago. 
He is or was collaborating with David Rogers at MSI to devise genetic
partial least squares.

Presumably you also know of Johnny Gasteiger's work, extensive, in this area.

Yvonne Martin

============================================================================
===========
--
Dr. Douglas A. Smith, President and CEO     |  voice: (814) 262-9091
The DASGroup, Inc.                          |    fax: (814) 262-9337
P.O. Box 5428                               |  email: [email-masked]
Johnstown, PA 15904-5428                    |     

Contract R&D specialists in computational chemistry, process modeling,
synthesis and design of novel compounds for chemistry, materials science,
and biotechnology.