[LON-CAPA-users] [Fwd: [Open Babel] ANN: Frog donates code to OpenBabel for SMILES to 3D conversion]

Jim Maxka lon-capa-users@mail.lon-capa.org
Fri, 19 Oct 2007 14:15:09 -0700

Greetings from medschool -- Here is an interesting development.  Most of 
our organic molecules are stored in the smiles format.  Getting 
conversions directly from the smiles format to a viewable form has 
required lots of work and has never really been gpl until now.

We all know that loncapa is the best cms for chemistry already.  If we 
could include this package, I think that it would make our package that 
much stronger.

Would there be any interest in working on this?  I think at least one 
Guy would give it a thought.
Thanks -- Jim

-------- Original Message --------
Subject: 	[Open Babel] ANN: Frog donates code to OpenBabel for SMILES to 
3D conversion
Date: 	Fri, 12 Oct 2007 16:12:38 +0100
From: 	Noel O'Boyle <baoilleach@gmail.com>
To: 	openbabel-discuss list <openbabel-discuss@lists.sourceforge.net>

Dear all,

Recently, researchers at the French research institutes INSERM and
CNRS developed an online service for converting SMILES string to 3D
conformers: "FRee Online druG 3D conformation generator (Frog)" at
http://bioserv.rpbs.jussieu.fr/Frog.html. A description of this
service was published in T. Bohme Leite, D. Gomes, M.A. Miteva, J.
Chomilier, B.O. Villoutreix and P. Tufféry. Nucleic Acids Research,
2007, 35, W568-W572 (http://dx.doi.org/10.1093/nar/gkm289):

"Frog is an on-line service aimed at generating 3D conformations for
drug-like compounds starting from their 1D or 2D descriptions. Given
the atomic constitution of the molecules and connectivity information,
Frog can identify the different unambiguous isomers corresponding to
each compound, and generate single or multiple low-to-medium energy 3D
conformations, using an assembly process that does not presently
consider ring flexibility. Tests show that Frog is able to generate
bioactive conformations close to those observed in crystallographic

On behalf of the OpenBabel project, I am pleased to announce that Dr.
Bruno Villoutreix (INSERM, University of Paris 5) and Dr. Pierre
Tufféry (INSERM, University of Paris 7) have generously donated their
code to OpenBabel. This code will be incorporated into OpenBabel under
the GPL in the coming months, making fast and accurate SMILES-to-3D
conformer generation available to the open source community for the
first time.

The absence of an open source 3D conformer generation algorithm has
increasingly become a problem in recent years due to the popularity of
SMILES strings for the description of molecular information.
Fortunately, this problem has now been solved. Thanks again to all
those involved in the development and release of this code.

For further information on Frog, please contact the corresponding
author of the Frog paper.


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