NCI PLATED Compounds Conversion

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Profile Jack Shultz

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Message 249 - Posted: 12 May 2009, 16:09:37 UTC

Wow we are cutting through this analysis at warp speed. I we can provide these results to TSRI so they can improve their scripts and or perhaps store them on a public repository for other researchers.
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Profile Tim Turner

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Message 251 - Posted: 12 May 2009, 16:20:01 UTC - in response to Message 249.  

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Andrew VoronkovProject donor
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Message 416 - Posted: 16 May 2009, 5:17:08 UTC
Last modified: 16 May 2009, 5:18:38 UTC

Jack, plated compounds in mol2 format have for the researchers not much more sense than plated compounds in SDF format. Babel doesn't make 3D coordinates conversion. Such conversion as I know is made only by licensed software which can be used only offline because of copyright questions. I work now with two applications which we can use for this:
1) Concord 3D coordinates generator
2) OpenEye conformers generator
All of this software is licensed to our lab. We need to make some agreement with my lab or other labs which have such software or to get license from these companies directly.
These generators also need preprocessing by filtering of SDF files for lead-likeness. I have for this purpose our lab script written in TCL and also OpenEye has filter package.
It is also possible to use lead-like dataset from ZINC but still we'll need to make 3D coordinates generation for it. And their filter are not good enough.

It would be great if we'll get license from OpenEye as non-profit organization at least for offline use for database preparation.
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