Subject: CCL: Replies on Batch Substructure Searching

From: Paul Soper <[email-masked]>
Date: Thu, 17 Apr 1997 14:16:40 -0400

Many thanks to all those who replied to my question on
software for 2D substructure searching:

    A colleage of mine is looking for a non-interactive program
which will take two 2D structures, compare them, and say whether
one is present as a substructure in the other.  He wants to do a
large number of pair-wise comparisons, so batch operation is a
must.  He'd obviously prefer that the program be available
without cost.

Here are the replies:

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

The key in such an application is an efficient algorithm for
substructure matching. With such an algorithm available, it is
quite trivial to make the job done in a batch mode.

You can check the following paper for an efficient substructure
perception algorithm, but the source code is, unfortunately, not
free.

Lingran Chen and Wolfgang Robien: 
	MCSS: A New Algorithm for Perception of Maximal Common
	Substructures and Its Application to NMR Spectral Studies. 
	1. The Algorithm, 
	J. Chem. Inf. Comput.Sci., 1992, 32, 501-506. 

Hope this will help.

-Lingran

Lingran Chen, Ph.D.
Senior Scientific Programmer
MDL Information Systems, Inc.
14600 Catalina Street
San Leandro
CA 94577

Phone: (510) 895-1313, Ext. 1305
FAX:   (510) 614-3616

Email: [email-masked]
URL:   http://www.mdli.com
       http://syngen2.chem.brandeis.edu/~chen/lingran.html

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

Tripos' Unity will do this, although not at zero cost.

Cheers,

Dave

Dr. David A. Winkler                      Voice: 61-3-9542-2477
Principal Research Scientist              Fax:   61-3-9543-8160
CSIRO Division of Chemicals and Polymers  http://www.csiro.au
Private Bag 10,Clayton South MDC,         http://www.wark.csiro.au
Clayton 3169, Australia

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

Can't help you with the "without cost" part, but this is
definitely possible with CS ChemFinder for Windows and a smidgen
of Visual Basic.  I've done it.  You should have no problem doing
several thousand to several tens of thousands of pairs an hour,
depending on how fast a machine you're using.  More information
about ChemFinder is available from http://www.camsoft.com, or
from me in a pinch.

Jonathan Brecher
CambridgeSoft Corporation
[email-masked]

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Paul Soper                        All the usual disclaimers apply
DuPont Central Research             [email-masked]  
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