Subject: Re: CCL:Enumeration / SMILES handling software

From: Andras.Borosy..at..givaudan.com
Date: Tue, 11 May 2004 07:48:34 +0200

Dear Colleague,

Try Jchem!

http://www.chemaxon.com/

Regards,

Andras Borosy
PhD Computational Chemist
Givaudan Schweiz AG
Fragrance Research
Ueberlandstr. 138
8600 D|bendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy..at..givaudan.com

"Mark Mackey" <m.mackey..at..cresset-bmd.com>
Sent by: "Computational Chemistry List" <chemistry-request..at..ccl.net>
10.05.2004 16:20

        To:     <chemistry..at..ccl.net>
        cc: 
        Subject:        CCL:Enumeration / SMILES handling software

Hi all.

Ib  re looking at quickb  nb  dirty ways to enumerate some libraries for a 
database. There seem to be hundreds of commercial library enumeration 
tools out there, most of which are horribly overpriced for what they do 
:). All we want is to enumerate a couple of libraries reasonably quickly 
and get the resulting molecules either as OKish 3D structures or as 
reasonable 2D structures. Enumerating libraries in SMILES space is 
trivial, but thereb  s a lack of tools available to do the coordinate 
generation.

So, does anyone know of a free/cheap tool that will either
(a) enumerate simple libraries into, say, SDF files, or
(b) generate 2D or 3D coordinates for SMILES strings.

I know that Corina et al. do (b), but we don't really need very good 3D 
coordinates (the molecules are going to be subjected to conformational 
searches and minimisation) so it's overkill and overexpensive for what we 
want.

Mark.

-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: 
line
and send your message to:  CHEMISTRY..at..ccl.net

Send your subscription/unsubscription requests to: 
CHEMISTRY-REQUEST..at..ccl.net 
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow..at..nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

---

From: "Joerg K. Wegner" <wegnerj<<at>>informatik.uni-tuebingen.de>
Date: Tue, 11 May 2004 08:25:05 +0200

Hi Mark,

i know only three 'usable' free appraoches:
1. CACTVS from W.D.Ihlenfeld (tcl, no source code for a low price), but 
maybe the best free tool out there.
http://www2.ccc.uni-erlangen.de/software/cactvs/

2. CDK: SMILES with 2D generation
http://sourceforge.net/projects/cdk/

3. JOELib: SMILES and interface to CDK (2D) and Ghemical (3D, simple all
atom force field)
joelib.sf.net

Interesting commercial approaches are:
- 2D: a new tool of Rarey et al.
http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci049958u
- 3D: OMEGA with OEChem as chemistry kernel (formerly called OELib) 
http://www.eyesopen.com/
So they have a good and advanced chemistry and computer science design 
(C++, object oriented, source code available, if you pay for their work).

- 2D: http://www.chemaxon.com/marvin/ (good programming interface)
- 3D: MOE for energy minimization (MMFF94 all-atom pair force field) in 
batch mode
http://www.chemcomp.com/

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:wegnerj<<at>>informatik.uni-tuebingen.de
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

---

From: Ferenc Csizmadia <fcsiz)at(chemaxon.com>
Date: Tue, 11 May 2004 16:38:16 +0200

Mark,

I suggest to check out our tools MolCoverter and Reactor.

Using MolConverter you can interconvert between file formats (like from 
SMILES to SDF) and generate 2D or 3D coordinates.
http://www.chemaxon.com/marvin/doc/user/molconvert.html
MolConverter is free if you don't build it into custom applications. It 
is available in the Marvin Beans and the JChem package. (Marvin Beans is 
easier to install)

You can use Reactor to enumerate virtual libraries using reaction modelling.
http://www.jchem.com/doc/user/Reactor.html
Movie: http://www.chemaxon.com/demos/flash/reactor.html
Reactor is included in the JChem package.

You can download these packages from our web site.
http://www.chemaxon.com/products.html

Best regards,
Ferenc

>Hi all.
>
>Ib  re looking at quickb  nb  dirty ways to enumerate some libraries for
>a database. There seem to be hundreds of commercial library enumeration