[Dock-fans] de novo drug design

John J. Irwin jji at cgl.ucsf.edu
Wed Jul 16 12:10:33 PDT 2008


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.


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.
> Thanks!
> -DX
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