[Dock-fans] de novo drug design

John J. Irwin jji at cgl.ucsf.edu
Thu Jul 17 10:15:55 PDT 2008


Hi DX

Cactvs is at http://xemistry.com/.

John


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 
> <mailto: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 <http://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.
>
>         Thanks!
>
>         -DX
>         ------------------------------------------------------------------------
>
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>
>


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