Subject: RE: programs for generation of topological indices

From: "Clair W. Cabal" <[email-masked]>
Date: Mon, 23 Oct 2000 12:42:11 -0600

I have received a couple of requests to share the information I received in
responses to my query.  Thank you very much to those who took the time to
send me information.

My original message is followed by a summary of the responses:

Date: Mon, 16 Oct 2000 13:04:01 -0600 (MDT)
From: Clair W Cabal <[email-masked]>
To: [email-masked]
Subject: programs for generation of topological indices

All,

Please forgive me if this is a redundant request, but in reviewing the
archives, I don't see much on this topic since 1995.

I am in search of a stand alone program to generate a very large number of
toplogical indices for chemical compounds.  I know of, but am not familiar
with MOLCONN-X, QuaSar-Descriptor and Dr. Basak's POLLY 2.3.  A respondent
to this query posed in 1995 mentioned a program called EMMA which could
handle up to 2,000 descriptors, but I have not received a response to
an inquiry about this from the developer at Moscow State University.

I would appreciate any feedback about use of the above mentioned programs
and any information about others that may have been developed more
recently. 

Thank you.

Clair Cabal
Research Assistant
Machine Learning Research Lab
Department of Computer Science
University of Montana
Missoula, Montana
email: [email-masked]
fax:  (406) 243-5139
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Date: Tue, 17 Oct 2000 08:58:58
From: "Rob Williams" <[email-masked]>
To: "'Clair W Cabal'" <[email-masked]>
Subject: RE: programs for generation of topological indices

Hi Clair,

Oxford Molecular distributes a product called TsarBatch. It is
a stand-alone version of the descriptor generation parts of their
Tsar QSAR product. I wasn't sure from your e-mail whether you were
after a program that calculates a very large range of descriptors,
or one that calculates standard topological indices for a very
large number of structures. TsarBatch is more in the latter of
these two categories. You can find more information at:

http://www.oxmol.com/software/tsarbatch/

There is a fact sheet that you can download from there.

Hope this is of interest to you.

Best regards,
Rob
                ------------------------------

Date: Tue, 17 Oct 2000 07:30:06
From: Doug Henry <[email-masked]>
To: "[email-masked]'" <[email-masked]>
Subject: FW: programs for generation of topological indices

The Dragon program was recently posted.  It takes Sybyl Mol2 and Hyperchem
hin files, and can generate  800+ descriptors.  It can be used in
conjunction with Babel, but I found the resulting files must have extra
blanks removed from the files to be acceptable to Dragon.  It can take a
directory of molecule files, generate a file with descriptor values, then
allows you to add your own "Y" colums to the data:

Dear Colleague,
                        We would like to advertise that the new software
DRAGON (version 1.0) for the calculation of 853 theoretical molecular
descriptors is now free downloadable from our Website.

This software has been produced by us, coherently to the Handbook of
Molecular Descriptors, by Roberto Todeschini and Viviana Consonni, edited in
these days by WILEY - VCH, in the Series of Methods and Principles in
Medicinal Chemistry, Vol. 11 (Editors: R.Mannhold, H.Kubinyi, H.Timmerman);
pp.680.

We have also activated a bibliographic reference service about molecular
descriptors at our Website and a special e-mail address
([email-masked]) for the exchange of information of the researchers
in this field.

Best regards,
                        Roberto Todeschini and Viviana Consonni

----------------------------------------------------------------------------
--------
Milano Chemometrics and QSAR Research Group
Department of Environmental Sciences
P.za della Scienza, 1 - 20126 Milano (italy)
WebSite: http://www.disat.unimib.it/chm/

[email-masked]
(just a user)

                ------------------------------

Date: Wed, 18 Oct 2000 11:38:07
From: "Vladimir A. Palyulin" <[email-masked]>
To: [email-masked]
Subject: descriptors

Dear Clair Cabal,

Just a few days ago Milano Chemometrics group headed by Professor
Roberto Todeschini released free version of DRAGON program which
computes about 850 descriptors. It can be downloaded from:
http://www.disat.unimib.it/chm/

Sincerely,

Vladimir Palyulin,
Head, Group of Computer Molecular Design,
Department of Chemistry,
Moscow State University

P.S. EMMA program was oriented for DOS and was developed in 1988-1993,
now we are working on Windows program which computes thousands
descriptors, which are treated with neural networks.

                ------------------------------

Thanks also to Elena Fioravanzo for forwarding information about DRAGON.

I should mention that DRAGON does not just produce topological indices, but
generates 14 classes of theoretic descriptors including geometric,
information theoretic, constitutional and BCUT descriptors to name a few.  I
have run some test data with DRAGON and find it to be very easy to use.  Now
my task is to convert existing data into mol file format!

Clair Cabal