The pharmacophore matching was described in a CDK News issue - but all the
links I have seem to be dead. It's very simplistic in fact - pharmacophore
query atoms and bonds are defined as subclasses of SMARTS atoms and bonds.
The query is parsed into a pharmacophore molecule and then a match is
identified via subgraph isomorphism. Currently only distance and angle
constraints are supported. The code really should be extended to support
dihedrals and excluded volumes
Regarding the details of the definition file - are you referring to the
definition in this particular case? Or just, generally how to define a
pharmacophore? If the former, it's probably best to get in touch with John
Van Drie directly.
Egon/Chris - do we have old versions of CDK News somewhere?
On Wed, Apr 29, 2015 at 3:36 AM, Tim Dudgeon <[email protected]> wrote:
> Nice!
> Is there any information available about the methodology involved and on
> the details (not xml schema) of the pharmacophore definition file?
>
> Tim
>
> On 28/04/2015 23:34, Rajarshi Guha wrote:
>
> I recently updated the CDK pharmacophore search tool (
> https://github.com/rajarshi/cdkpcore) and got this comment from a very
> happy user :)
>
> Kudos to everybody who contributed to the significant improvements in
> the CDK.
>
> ---------- Forwarded message ----------
> From: John H Van Drie <[email protected]>
> Date: Tue, Apr 28, 2015 at 4:58 PM
> Subject: CDKPsearch speed
> To: [email protected]
>
>
> Rajarshi
>
> I'm amazed at the speed of CDKPsearch now. 1 million confs in 3 min,
> using 15 processors. It's not compute-bound, so I think if I shift things
> to my fastest disk things will be even better.
>
> Almost interactive!
>
> Of course, now I'll want to use more confs/mol...
>
> John
>
> Van Drie Research LLC
> www.vandrieresearch.com
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
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