Subject: qsar - summary

From: [email-masked] (Computational Chemistry List)
Date: Tue, 4 Oct 1994 17:36:39 +0100 (MET)

Hi netters!

A couple of weeks ago I started an inquiry about PD (what means Public
Domain, 8-)) and non-PD software. Now I will summarize the received
answers (as promised). Thanks to everybody, who helped me.

My original question:
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Hi netters!

I am searching for a program (PD preferred, but not absolutely necessary) for 
QSAR analysis (PC or SGI INDY with IRIX 5.2). I also need a little help in 
exploring the method, that means information about books and articles for 
beginners. I hope, I am not boring you with a question discussed often before. 
I looked for 'QSAR software' in the osc index files of 91-93 and didn't find 
much, so I think, I can run the risk of asking this question 8-)

Naturally I will post a summary if desired.

Thanks in advance

Kay Kreidler
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An now the answers: [my comments in brackets].
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To: Kay Kreidler
Re: QSAR software

If you would be kind enough to send me your address, I will have someone send
you our literature on the QSAR software that we can provide within our Cerius2
environment.  

[I suppose, my .signature wasn't working. So I apologize for the missing
information.]

Along with an extremely easy to learn/use user interface, our
QSAR functionality supports a variety of linear regression techniques (simple,
stepwise, PLS) in addition to a novel genetic algorithm techniques that can
provide a family of QSAR equations that can be non-linear.  Cerius2 supports
46 descriptors "out of the box", and users are able to add new descriptors as
their work requires.  Descriptors can also be derived from a pseudo-receptor
model for the active site.

I look forward to hearing from you.

[I received the information from Karen Faulkner of MSI]

------

Scott D. Kahn, Molecular Simulations Inc.        (408) 522-0100
Email : [email-masked];                   FAX  (408) 522-0199
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 I would really like to receive information about
your request. QSAR on IRIX 5.2.
           Yours truly,
        
           Ramiro Arratia-Perez
           Facultad de Quimica
     Pontificia Universidad Catolica de Chile
     [[email-masked]]
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Kay:

	Would you please post a summary of PD QSAR software?  I would appreciat
it.
John.

John J. Isbell
Department of Chemistry 
University of Texas at Austin                  Voice:  (512) 471-0041
Austin, Texas 78751				 Fax:  (512) 471-8696

Email:          [email-masked]
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The Sybyl modelling package has this built in, together with their excellent 
CoMFA method for 3D-QSAR.  Runs on SGI machines.  Contact [email-masked].

Cheers,

Dave

[I tried to contact this address, but there was no response until today.
Any suggestions?]
__________________________________________________________________________

   Dr. David A. Winkler                        Voice: 61-3-542-2244      
   Principal Research Scientist                Fax:   61-3-543-8160      
   CSIRO Division of Chemicals and Polymers
   Private Bag 10       
   Clayton, Australia.

   "Life is what happens to you while you're making other plans"
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First of all I'm not aware of any public domain (PD) software for QSAR, unless 
you count "pieces" like PD stat packages. The only software that I'm aware 
of that is specific for QSAR for the PC is a program called QSAR-PC from 
Biosoft. It has some rudimentary regression routines coupled to a substituent 
property database that can be used to assemble data tables. It is menu 
driven and will do Hansch and/or Free-Wilson analyses. This program is fairly 
affordable, ~US$199  but not as comprehensive as some of the others below, 
(the others below are also *much* more expensive $$$).
Contact:  Biosoft, PO Box 580, Milltown, NJ 08850   201/613-9013
     or   Biosoft, 22 Hills Road, Cambridge CB2 1JP, UK  0223 68622

For the SGI there is the QSAR module in Sybyl which performs Comparative 
Molecular Field Analysis, (CoMFA) but doesn't handle more traditional QSAR 
without having to piece together data sets from somewhere else. It does have
tools for PLS, PCA & Cluster Analysis, but few property calc's and no
substituent property database.
Contact:  Tripos Assoc., 1699 Hanley Rd., St. Louis, MO 63144 USA
phone:  314-647-1099

There is a QSAR program from Oxford Molecular for the SGI that is specifically
aimed at QSAR from several viewpoints called TSAR. This is the most complete
QSAR package I have seen for specifically addressing QSAR. It has substituent
methods and property databases as well as means to calculate a bunch of 
properties useful for QSAR. TSAR has a large number of statistical treatments 
and graphical means all in one place, which makes it quite valuable. 
Neural nets are being added and it can read files from other modeling pkgs.
Contact: Oxford Molecular, 7005 Backlick Ct, Suite 200, Springfield, VA 22151
phone: 703-658-4854

As for fundamental literature to get started I would take a look at a few of 
these...

[ Books ]

"QSAR: Hansch Analysis and Related Approaches", Hugo Kubinyi, VCH, NY, 1993.
   (very good references)

"Quantitative Drug Design - A Critical Introduction", Y. Martin,
 Marcel-Dekker, NY 1978.
 (also very good for fundamentals, however it is out-of-print,)
 (but your library may be able to get it through inter-library loan.)

[ Papers ]

C. Hansch and T. Fujita, JACS, 86, (1964), 1616.              -|
                                                               |-classics
J. Topliss and R. Edwards, J. Med. Chem., 22, (1979), 1238.   -|

C. Hansch, Acc. Chem. Res., 26, (1993), 147.                  -|
                                                               |
J. Topliss, Perspect. in Drug Dis. and Des., 1, (1993), 253.   |-good overviews
                                                               |
S. Wold, QSAR, 10, (1991), 191.                               -|

Hope this helps to get you started!  Regards, Greg
+-----------------------------------------------------------------------+
| Gregory L. Durst Computational Chemistry | | phone: 317/337-3413
DowElanco R&D | | email: [email-masked] 9330 Zionsville Rd.  Bldg
306/D2 | | Indianapolis, IN 46268 USA |
+-----------------------------------------------------------------------+
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Kay, 
 A nice program for QSAR is distributed by Oxford Molecular it is
called Tsar. Other than that I would recommend take any package of
statistics that would let you perform multivariate analysis and fed it
your own properties.  REFERENCES: C Hansch and TE Klein Acc Chem Res
19:392(1986) T Fujita In Comprehensive Medicinal Chemistry Vol. 4,
Pergamonm 1990.  H Kubinyi same as above.  LH Hall and LB Kier Reviews in
Computational Chemistry Vol1, VCH, pp 367-422.  R. Franke, Theoretical
Drug Design Methods, Akademie Verlag, 1984.

If you were thinking of 3D QSAR, RD Cramer etr al. JACS 110:5959 (1988) GR
Marshall& RD Cramer, Trends in Pharm. Sci. 9: 285 (1988) Then you should
contact TRIPOS Assoc. They are the ones that sell COMFA, the typical 3D
QSAR program.   

Regards, Hugo O. Villar. 
Terrapin Technologies, Inc. 750-H
Gateway Blvd. So. San Francisco, CA 94080. 
Phone (415) 244-9303. 
Fax (415) 244-9388
[[email-masked]]
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If you can find a copy, read my 1978 book which others say was a real
help to them getting started.  Of course it is old...I am starting to
revise it.

Title is Quantitative Drug Design. Publisher is Marcel Dekker.

As to software, there is quite a bit. I haven't used much of it because
I am much more into molecular modeling...  However, Oxford Molecular
sells TSAR which looks pretty nice to me. I think the parameters are
already in it.  With Sybyl one can load in parameters or type them in
and run sophisticated analyses from a molecular spreadsheet.  Of course,
it has the advantage that one can also do CoMFA 3D QSAR in the same context.

  @@@@@@@@@@@      Yvonne Martin, Senior Project Leader
             @     Computer Assisted Molecular Design Project
   @@@@@@@@  @     D-47E, AP9A-LL
  @          @     Abbott Laboratories
  @          @     One Abbott Park Road
   @@@@@@@@@@      Abbott Park, IL 60064
                   Phone: 708 937-5362 FAX: 708 937-2
                   [[email-masked]]
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REGARDING                QSAR
Dear Kay,

Your recent query to the CCL about QSAR software has been forwarded to me by a
colleague. I hope that you don't mind getting replies from commercial
companies!

You may already be aware that the latest release of Cerius2 this month includes
a suite of modules for Drug Discovery. This includes the C2 QSAR module, very
straightforward and easy to use for generating quantitative structure-activity
relationship models.  Cerius2 also makes it very easy to use Molecular Shape
Analysis, an extension of QSAR for generating quantitative measurements of
molecular shape properties.  
The use of Genetic Algorithms to generate multiple QSAR models increases the
likelihood that the best structure-activity relationships have been found.

If I may, I will send an information pack by post. Do not hesitate to contact
me if we can be of further assistance.

Best regards
Karen Faulkner

-------------------------------------------------------
Karen Faulkner
Academic Account Manager
Molecular Simulations
240/250 The Quorum, Barnwell Road,
Cambridge, CB5 8RE, England
Telephone:  + 44 223 413300
Fax:  + 44 223 413301

email: [email-masked]
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That's all, folks. Again, thanks for your help. Now I have to make the
decision, what to do... Unfortunately, it seems, that there is not enough
money for such an expensive program.

Kay Kreidler
Department of Inorganic Chemistry
Heinrich-Heine-University Duesseldorf
Universitaetsstr. 1
40225 Duesseldorf
Germany
e-mail: [email-masked]