Question: What Free Databases Are Available To Store Enantiomers Information?
1
gravatar for David
7.5 years ago by
David70
David70 wrote:

Hello, i'm looking for free/open source chemical databases or at least his database schema, to store chemical structures (name, SMILES, InChi, 2D, 3D...) with his enantiomers. I mean, a structure with the same name and SMILES, but different 2D and 3D coordinates information.

Thank you.

database • 1.4k views
ADD COMMENTlink modified 7.5 years ago by Wolf Ihlenfeldt150 • written 7.5 years ago by David70

??? Properly encoded names, InChI, SMILES with stereo information should be different for enantiomers, not the same...

ADD REPLYlink written 7.5 years ago by Wolf Ihlenfeldt150

I mean, with a certain SMILES, if you assign 3D coordinates (with OpenBabel, CORINA...) sometimes you can retrieve several rotamers and enantiomers. For this situation, i would like to know how is the best way to store the info. An unique ID for each enantiomer or not? how to define the relation between the rotamers in the database schema?

ADD REPLYlink written 7.5 years ago by David70
1
gravatar for Wolf Ihlenfeldt
7.5 years ago by
Wolf Ihlenfeldt150 wrote:

The Cactvs toolkit www.xemistry.com/academic free version for academic/educationa/private use) can store an arbitrary and variable number of 3D coordinate sets per structure in its query-optimized native file formats (cbs, bdb).

If you are going for a traditional SQL database, it would be simple to have separate core structure and 3D coordinates tables, with a standard 1:n mapping via an identifier between the tables.

ADD COMMENTlink written 7.5 years ago by Wolf Ihlenfeldt150

Thank you for the information: i'm using MySQL. Right now i'm analyzing ChEMBL 11 [1] and VSDMIP 1.5 [2] database schemas to get some ideas.

[1]http://cactus.nci.nih.gov/blog/?p=1435 [2] http://www.springerlink.com/content/d821tx201783652r/

ADD REPLYlink written 7.5 years ago by David70
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