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

Ray Batchelor lon-capa-users@mail.lon-capa.org
Fri, 18 Jan 2008 09:47:23 -0800

Thanks for this posting, Jim.
Your past contributions and continued interest are very much appreciated.

Has anyone already started to work on this?
Please let me know, so that I don't try to reinvent the wheel...


On Oct 19, 2007 1:15 PM, Jim Maxka <jim.maxka@nau.edu> wrote:
> 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
> complexes."
> 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.
> Regards,
>   baoilleach
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Raymond J. Batchelor
Dept of Chemistry
Simon Fraser University