CCL: Summary of Program to search SD/MDL formatted files from chemical companies

Thank you all for all your responses and all your help.  I greatly
 appreciate everything.  Have a great day.
 The chemoinformatics toolkit CACTVS has very powerful substructure
 search capabilities.  It is free for academic use.  See
 We have, e.g., based our online Enhanced NCI Database Browser
 ( on it.  We are using
 search in SD files numbering in the millions of compounds (although you
 get a huge additional speedup if you first convert them into the
 internal CACTVS format).  We are working to put a more complete CACTVS
 documentation together - if you are interested, feel free to contact me.
 For all other questions, please contact the author of CACTVS,
 Wolf-Dietrich Ihlenfeldt (wdi|at|
 If you need a chemically intelligent database solution that can also be
 used to build an intra- or internet application, please check out JChem
 You can try it here:
 JChem can be downloaded from the site. An example application that can
 be easily customized is included in the package.
 The software is in Java so it is portable. It can be connected to
 several databases, like  MySQL, PosgreSQL, Oracle, etc.
 Best regards,
 If you look for a free substructure search program, try obgrep which is
   a tool available at the open babel sourceforge web site
 The program uses daylight SMART chemical language to perform the query
 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
 the Omega from Openeyes ( might do what you ask
 looking for, and is free for academics, as far as I know.
 The CACTVS Chemoinformatics toolkit, which contains a full and
 competitive substructure search engine, is free for academic use and can
 be downloaded from This engine drives the NCI
 database ( This is not a graphical
 environment, but a script tool (but because of this far more powerful
 than ISIS/Base - it reads ISIS query files and Daylighgt SMARTS, though)
 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
 Feel free to contact the CDK development team on the
 cdk-devel|at| mailing list to discuss whatever
 CDK-related question you have.
 Hi, Don,
 CACTVS is a freely available chemical extension of the Tcl scripting
 language [].
 There are some commands to allow you to search chemical database files
 (either within a flat file or from a DBMS).
 Although a powerful language, the main drawback is the lack of
 Consequently, I am attaching a PDF of the beginning of a manual I was
 trying to create from notes of some of our group members here.
 I warn you that it is incomplete (and on hold indefinitely, as
 priorities have shifted) and may not be totally accurate from a
 conceptual viewpoint.  However, that said, something is better than
 nothing so...  Also, towards the end of the manual I have just added the
 structure searching notes verbatim.
 Hope the information helps,
 Hi Donald,
 MarvinView can search SD files <>;
 Hope this helps
 Best regards