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Re: retrosynthesis

Hi Stephan,

On Sun, Jul 22, 2012 at 9:46 PM, lloyd riggs <lloyd.riggs@gmx.ch> wrote:
> I'm trying to find GPL retorsynthesis software, such as LHASA or WODCA.  As it seems all of the freeware I knew from 2002 is gone, and only 1 commercial version I could find cost several thousand dollars, I woundered if anyone had an old LHASA GPL version or equivalent for Linux/Unix.

Retrosynthesis is an interesting and important application indeed. I
have been author of various open source chemistry tools, one being the
Chemistry Development Kit (CDK) [0]. "We"d love to have
retrosynthesis, and the CDK has all the cheminformatics tools to do it
(e.g. [1]). The CDK is packaged as libcdk-java.

However, what is missing, is the *Open* reaction data. This is why
they can make that software so expensive: they sit on a pile of hidden
reaction data. As soon as we have a reasonably sized reaction
database, or at least with 99% of the 80% most commonly used
reactions, then we can easily make a tool like that.

Sadly, there are few cheminformaticians who have time for this. As an
academic, you do not get any funding for this. Because, obviously, the
problem has already scientifically been addressed. But the number of
people who like to hack on cheminformatics in their free time, you can
count on one hand.

If you like to take this forward, and get this done, this is what we need:

1. CMLReact as format to store reactions
2. a tool to create such reactions (JChemPaint/Bioclipse come to mind,
and are pretty close)
3. an online database to act as repository of such CMLReact files

>From there on, it's downhill. The Blue Obelisk community would be the
place to do this [2].




Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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