CCL: chemical databases search using multiple substructures, is it available somehwere?


I think that should actually work in PubChem, if they have not changed the defaults of the structure match engine.

Just enter multiple fragments in one record. Reported matches contain both fragments, without overlap . If this is not the case, the defaults were changed. PubChem, in order to keep the user interface manageable, only exposes a small fraction of the engine capabilities, so the desired behaviour may not be accessible via this path.

If you need more control on the match process, you can download the Cactvs toolkit (www.xemistry.com/academic for academic/educational use, commercial users need a license). This is the match engine behind PubChem. With the full scriptable matcher, there are many additional facilities to control the match process on your own data files (and/or/xor of multiple fragments, fragment overlap control, etc.). Matches can be performed with identical syntax both on standard data files (SDF,SMILES, InChI, MOL2, albeit slow) or optimized query files (cbs or bdb formats, invest time once to compute screens, etc, but after that, queries are much quicker)

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On Fri, Dec 16, 2011 at 7:55 PM, Andrew Voronkov drugdesign],[yandex.ru <owner-chemistry.:.ccl.net> wrote:

Sent to CCL by: Andrew Voronkov [drugdesign=-=yandex.ru]
Dear CCL users,
I am regularly using PubChem to mine databases using Substructure search, when as substructure I usually use key pharmacophore containing fragment.
Is that possible to use two or several fragments not connected into one structure?
There are software Âtools like in BioSolve IT or OpenEye for bioisosteric linker search between two fragments, I have somehow similar task, I need to enter two pharmacophore containing fragments and find in databases of catalog compounds all the structures which contain both of these fragments.

Can anyone recommend me what can I use for such multiple-substructure search through chemical databases?

Best regards,
Andrew



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