Subject: SUMMARY - Software for combinatorial generation of structures

From: <gustavo:at:mercury.chem.pitt.edu>
Date: Mon, 27 Jun 2005 21:00:16 -0400 (EDT)

Dear CCL Readers,
     here you have a summary of my recent request for a software for
combinatorial generation of structures.
     Some of the answers deal with virtual synthesis and are more
sophisticated than I had in mind. The kind of structures I am
planning to generate are related by a common heterocyclic skeleton
containing different groups (N(CH3)2, NO2, CH3, OCH3, etc) connected
to it. They are not related by a chemical reaction.
      The conversion of the AUTOBUILD program to work under Linux
would be complicated by the fact that most of the changes would
involve graphical routines and I wouldn't know how to convert the
routines from Silicon Graphics to Linux.
      I have decided to generate my structures using SMILES and
then converting them to XYZ.
      Once again I would like to say thanks for all the answers
I have received. Sincerely yours,
                             Gustavo L.C. Moura
                         gustavo:at:mercury.chem.pitt.edu
--------------------------------------------------------------------------------
ORIGINAL MESSAGE

Dear CCL Readers,
     I am looking for a program capable of generating structures of
molecules in a combinatorial way. In other words, I want to be able to give a
template and a series of fragments to the program and having the program to
generate all the structures that can be obtained by connecting these
fragments
to the template. The program should be able to write the final structures
in a
format that can be converted to be read by the MOPAC program for optimization
of geometry. I would like to be able to run such a program in a machine with
Linux or, perhaps, Windows operating systems. Any suggestions are welcome,
but
I would prefer a free for academia program.
     I have already found in the INTERNET the AUTOBUILD program that is
distributed by the INTERPROBE CHEMICAL SERVICES company
(http://www.interprobe.co.uk/inter/interprobe.html). Unfortunately, the
AUTOBUILD program works only on Silicon Graphics machines.
     Thank you very much in advance. Sincerely yours,
                                             Gustavo L.C. Moura
                                         gustavo:at:mercury.chem.pitt.edu

---------------------------------------------------------------------------------
Konrad Koehler <konrad.koehler @ karobio.se>

Dear Gustovao,
One possible solution relying on perlmol (http://www.perlmol.org/) and SMARTS
substructure notation
(http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) to define
reactant
functional groups may be found on the following web site:

http://www.perlmol.org/examples/

I would be interested in reading a summary of your responses.  Best regards,

Konrad

---------------------------------------------------------------------------------
Armel Le Bail <alb @ cristal.org>

See a list of programs in this paper;
http://journals.iucr.org/b/issues/2002/04/00/bk0108/bk0108.pdf
Though they may not completely fulfill your dreams...

For inorganic compounds, see:
http://journals.iucr.org/j/issues/2005/02/00/cg5019/cg5019.pdf
and references inside.

Best wishes,

Armel Le Bail

----------------------------------------------------------------------------------
Jeremy R. Greenwood <jgreenw @ speakeasy.net>

Dear Gustavo,
The forthcoming Schrodinger release later this year will include a new
product,
CombiGlide, which can do all of the above and more (with some intelligent
machinery
> from ligprep to cut down on knotting for example, handle pKa, stereochemistry
tautomerism, etc.). Primary platform is Linux. GUI or command-line.
Dicounted but not free for academic research, though it's free for teaching.

Hope this helps,

Jeremy

-----------------------------------------------------------------------------------
John Bushnell <bushnell @ chem.ucsb.edu>

Hi,

   I took a quick look at the site below, and you can freely download
the source code for Autobuild.  It gives all kinds of errors if I try:
g77 autobuild.f
on a Linux machine here, but it may be possible to clean up the code
so that it will compile correctly, and/or play with compiler flags to
make this work.
   So...if you've got somebody who is familiar with Fortran, you could
probably get this to work.  But it will require some time and effort.

          - John

------------------------------------------------------------------------------------
Tim Aitken <taitken @ accelrys.com>

Dear Dr Moura,

I read with interest your posting on CCL net regarding combinatorial tools
for library enumeration. We offer several solutions for this purpose,
using either reaction based or generic core (Markush) enumeration and have
software that operates on Linux, Solaris and Windows. The Combichem
Enumeration Components sound like they may be the right thing for you :
http://www.accelrys.com/products/accord/accordproducts/combichem_enumeration.html

Please contact me if you would like any further information, or discuss
specific requirements. If our solutions do not meet your needs I may be
able to point you in a more appropriate direction.

Best regards,

Tim

-------------------------------------------------------------------------------------
Gyorgy Pirok <pirok @ chemaxon.com>

Dear Gustavo,

I would like to draw your attention to a Java-based virtual synthesis
program of ChemAxon called Reactor. It is fast (up to 500k reactions/hour),
flexible (able to batch process reactions creating combichem libraries), and
smart (evaluates reactions containing chemo-, regio- and stereoselectivity
info). It supports a wide range of reaction an molecule formats, so I am
sure that you can easily integrate it with MOPAC. It is also worth to
mention, that all ChemAxon tools including Reactor is FREE for the academia
and include API. Some useful links:

Latest scientific poster about Reactor:
http://www.chemaxon.com/conf/Making_Real_molecules_in_virtual_space.pdf

Related user documentation:
http://www.jchem.com/index.html?content=doc/user/Reactor.html

You can download it from the www.chemaxon.com web site and require a FREE
Academic license in an email.

I hope, that you will have fun with it.

Best regards,

Gyvrgy