[Dock-fans] de novo drug design

Roe, Diana dcroe at sandia.gov
Mon Aug 18 10:09:51 PDT 2008


Thanks Scott for remembering BUILDER.  I'm afraid it is not currently maintained.  I've re-implemented the CombiBUILD features in PDock, the in-house docking tool I developed at Sandia which also implements both the Dock/autodock algorithms.

--Diana

-----Original Message-----
From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org] On Behalf Of Scott Brozell
Sent: Friday, August 15, 2008 5:52 PM
To: Dong Xu
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] de novo drug design

Hi,

I do not know about the availability or timeliness of these programs:

Scott C.-H. Pegg, Jose J. Haresco, Irwin D. Kuntz: A genetic algorithm for structure-based de novo design. Journal of Computer-Aided Molecular Design 15(10): 911-933 (2001)

Diana C. Roe, Irwin D. Kuntz: BUILDER v.2: Improving the chemistry of a de novo design strategy. Journal of Computer-Aided Molecular Design 9(3): 269-282 (1995)

Scott


On Wed, 16 Jul 2008, Dong Xu wrote:

> Hi John,
>
> Thanks for all the info! I will check them out. For Cactvs, is this
> the right link?
>
> http://www2.ccc.uni-erlangen.de/software/cactvs/index.html
>
> -DX
>
> On Wed, Jul 16, 2008 at 12:10 PM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
>
> > Hi DX
> >
> > I don't know of any free de novo design tools. I do know about
> > Allegrow http://bostondenovo.com/ and Sprout
> > http://www.simbiosys.ca/, but have no idea about price.
> >
> > For scaffold hopping, try ROCS/EON from OpenEye
> > (http://eyesopen.com/) which is a shape approach, and is free to
> > accredited academics. OE also have a tool for directly mutating one
> > atom at a time, BROOD, but it may be a challenge to test some of
> > those suggestions experimentally.  Cactvs is free to academics and
> > incorporates fingerprint methods that can be use to essentially
> > scaffold hop (find similar molecules).  molinspiration.com is free
> > to academics and has a tool to break up molecules into fragments, which is a useful underlying technology for scaffold hopping.
> >
> > Of course, none of these programs works directly with DOCK - I
> > interpreted your "can be used along with" liberally.
> >
> > John
> > UCSF DOCK Team
> >
> >
> > Dong Xu wrote:
> >
> >> Hi Dock fans,
> >>
> >> Are there are freely available de novo drug design tools that can
> >> be used along with Dock? I'm interested in tools that do
> >> core/scaffold hopping and pharmacophore.


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