CCL: Replies on Batch Substructure Searching
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:
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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: LCHEN (+ at +) MDLI.COM
URL: http://www.mdli.com
http://syngen2.chem.brandeis.edu/~chen/lingran.html
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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
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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
jsb (+ at +) camsoft.com
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Paul Soper All the usual disclaimers apply
DuPont Central Research soperpd (+ at +) esvax.dnet.dupont.com
P.O. Box 80328 Tel (302)-695-1757
Wilmington, DE 19880-0328 FAX (302)-695-2112
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