Just out of curiosity, I have seen many publications about scaffold tree
generation. Like the Scaffold Tree[1], Scaffold Hunter[2], inSARa,
Fragment-Augmented Molecular Hasse Diagrams, Snowflake Diagram[3]...
How do you guys choose among them? I haven't seen any comparison paper for
those methods, but I guess this is a subjective question..
[1] The Scaffold Tree − Visualization of the Scaffold Universe by
Hierarchical Scaffold Classification
[2] Interactive exploration of chemical space with Scaffold Hunter
[3] Analysis and Study of Molecule Data Sets Using Snowflake Diagrams of
Weighted Maximum Common Subgraph Trees
On Wed, Sep 2, 2015 at 6:01 AM, Axel Pahl <[email protected]> wrote:
> That's great news, thanks Nick (thesis always comes first!).
>
> Kind regards,
> Axel
>
> On 02.09.2015 11:35, Nicholas Firth wrote:
> > Hi Axel,
> >
> > Nathan is working on the publication at the moment. I've thought about
> the code and written a small portion of it, it won't take me too long to
> write (once I've submitted my thesis). So the code should coincide with
> submission of the manuscript.
> >
> > 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: Axel Pahl [[email protected]]
> > Sent: 02 September 2015 10:21
> > To: Nicholas Firth
> > Cc: George Papadatos; RDKit Discuss
> > Subject: Re: [Rdkit-discuss] generating scaffold trees
> >
> > Hi Nick,
> >
> > are there any news on this?
> > It would still be very interesting.
> >
> > Kind regards,
> > Axel
> > (and a great UGM to all attendees!)
> >
> > On 22.05.2015 17:31, Nicholas Firth wrote:
> >> We have an as yet unpublished method which is similar (but performs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
> >>
> >>
> >>
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