[Dock-fans] de novo drug design

Scott Brozell sbrozell at scripps.edu
Fri Aug 15 17:52:00 PDT 2008


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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