Subject: Program to search SD/MDL formatted files from chemical companies

From: "Donald Keidel" <dopetec:at:dslextreme.com>
Date: Mon, 27 Oct 2003 18:02:14 -0800

Hello,

I am looking for a program to search SD/MDL formatted files (chemical
company libraries of compounds).  I have found ISIS/Base and 3DFS, but I
was wondering if anyone knows of others that might be cheaper than
ISIS/Base (hopefully free), but commercial examples would be of great
help also.  Thank you in advance to anyone who reads and responds to
this request.  Have a great day.

Don

------------------------------------------------------------------------
---------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dopetec:at:dslextreme.com
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

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From: Christoph Steinbeck <c.steinbeck_at_uni-koeln.de>
Date: Tue, 28 Oct 2003 13:52:02 +0100

> this request.  Have a great day.

Don,

not sure what exactly you mean by "to search SD/MDL formatted files". 
Our open source java library for structural chemo- and bioinformatics, 
The Chemistry Development Kit (CDK) [1] can read SD/MDL files and 
perform a number of operations on it, like searching for a particular 
substructure, etc. Other operations, like calculating certain 
descriptors, can be quickly implemented.
The CDK lives on http://cdk.sourceforge.net.
Feel free to contact the CDK development team on the 
cdk-devel_at_lists.sourceforge.net mailing list to discuss whatever 
CDK-related question you have.

Cheers,

Chris

[1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E., 
Willighagen, E.; 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.

-- 
Dr. Christoph Steinbeck (e-mail: c.steinbeck_at_uni-koeln.de)
Groupleader Junior Research Group for Applied Bioinformatics
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..

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From: Fabien Fontaine <ffontaine~at~imim.es>
Date: Tue, 28 Oct 2003 15:01:53 +0100

If you look for a free substructure search program, try obgrep which is 
  a tool available at the open babel sourceforge web site 
http://sourceforge.net/projects/openbabel/
The program uses daylight SMART chemical language to perform the query 
(http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html)

Unfortunately, the program is not in the current release (1.100.1)
for the moment, but you can get it by anonymous access to the CVS 
repository.

Regards,
Fabien

Donald Keidel wrote:
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-- 
Fabien Fontaine
Engineer in Biotechnology
Computer-Assisted Drug Design Laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF

Passeig Maritim de la Barceloneta, 37-49	Tel: +34 93 224 08 94
E-08003 Barcelona (Spain)		       	Fax: +34 93 224 08 75
e-mail: ffontaine~at~imim.es			http://www.imim.es/grib