We have an as yet unpublished method which is similar (but performs better) implemented in RDKit. However we use MOE for the scaffold tree. It would be quite easy to implement in RDKit , but I have a thesis to write!
My suggestion would be to ask Nathan to write up the paper and then give you guys the code. Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter @ICRnews ________________________________________ From: George Papadatos [[email protected]] Sent: 22 May 2015 16:27 To: Axel Pahl Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] generating scaffold trees Hi all, Coincidentally, we had a chat about this with James the other day. Maybe the good colleagues at the ICR have implemented this already with RDKit? Nick? Cheers, g On 22 May 2015 at 13:38, Axel Pahl <[email protected]<mailto:[email protected]>> wrote: Dear RDKitters, has someone used the RDKit to generate scaffold trees from molecules as described in this paper: Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58 I know that this is possible with ScaffoldHunter and that there is a Pipeline Pilot component for it, but being able to do it in RDKit would fit especially well in my workflow... Kind regards and have a nice weekend, Axel ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud 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. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud 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. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
