Subject: Re: CCL:fingerprint generation software

From: "Sudhir Kulkarni" <sudhirk = = = VLifeSciences.com>
Date: Wed, 6 Apr 2005 23:26:05 -0500

"Molecular Design Suite (MDS)" can generate fingerprints and search for similarity. Following database search options are provided in MDS
- 2D substructure/template search
- 3D substructure/template search 
- Descriptor based search
- Fingerprint generation & search
- Pharmacophore generation & search
- Receptor based search

Please look at http://www.vlifesciences.com/Products.htm
and register for demo version.

Sudhir Kulkarni

---------- Original Message ----------------------------------
From: "Lei Wang" <lei.wang = = = louisville.edu>
Date:  Wed, 06 Apr 2005 12:06:24 -0400

>I want to generate finger-prints for my chemical database.  and want to use such info to do sub-structure or similarity search. What software could I use?
>
>Thanks!
>
>Lei
>
>
>
>
>-= This is automatically added to each message by the mailing script =-
>To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
>and send your message to:  CHEMISTRY = = = ccl.net
>
>Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST = = = ccl.net 
>HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 
>
>If your is mail bouncing from ccl.net domain due to spam filters, please
>use the Web based form from CCL Home Page 
>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>
>

________________________________________________________________
Sent via the WebMail system at VLifeSciences.com

---

From: Christoph Steinbeck <c.steinbeck=at=uni-koeln.de>
Date: Thu, 07 Apr 2005 10:10:41 +0200

> I want to generate finger-prints for my chemical database.  and want to use such info to do sub-structure or similarity search. What software could I use?

Dear Lei,

as Rajarshi has pointed out already, our Chemistry Development Kit 
(CDK), hosted at http://cdk.sf.net, can do what you are looking for [1].
I would like to add that the CDK is free software under LGPL license.
There is already a public web database running completely based on CDK, 
which is NMRShiftDB, our open-access, open-submission, open-source 
database for organic structures and their NMR data [2,3]. There, 
substructure searching is done with a prefiltering using CDK 
fingerprints, followed by a CDK substructure search in the result set.
NMRShiftDB is available to the public at http://www.nmrshiftdb.org.
Further, the well known BRENDA database 
(http://www.brenda.uni-koeln.de/) does substructure searching based on 
the CDK.

Cheers,

Chris

[1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E. et 
al. The Chemistry Development Kit (CDK): An open-source Java library for 
chemo- and bioinformatics. Journal of Chemical Information and Computer 
Sciences 2003, 43, 493-500. http://dx.doi.org/10.1021/ci025584y
[2] Steinbeck, C.; Kuhn, S.; Krause, S. NMRShiftDB - Constructing a 
Chemical Information System with Open Source Components. Journal of 
Chemical Information & Computer Sciences 2003, 43, 1733 - 1739. 
http://dx.doi.org/10.1021/ci0341363
[3] Steinbeck, C.; Kuhn, S. NMRShiftDB   compound identification and 
structure elucidation support through a free community-build web 
database. Phytochemistry 2004, 65, 2711-2717. 
http://dx.doi.org/10.1016/j.phytochem.2004.08.027

-- 
Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck=at=uni-koeln.de)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z|lpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..