<div dir="ltr">Hi John,<br><br>Thanks for all the info! I will check them out. For Cactvs, is this the right link?<br><br><a href="http://www2.ccc.uni-erlangen.de/software/cactvs/index.html">http://www2.ccc.uni-erlangen.de/software/cactvs/index.html</a><br>
<br>-DX<br><br><div class="gmail_quote">On Wed, Jul 16, 2008 at 12:10 PM, John J. Irwin <<a href="mailto:jji@cgl.ucsf.edu">jji@cgl.ucsf.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi DX<br>
<br>
I don't know of any free de novo design tools. I do know about Allegrow <a href="http://bostondenovo.com/" target="_blank">http://bostondenovo.com/</a> and Sprout <a href="http://www.simbiosys.ca/" target="_blank">http://www.simbiosys.ca/</a>, but have no idea about price.<br>
<br>
For scaffold hopping, try ROCS/EON from OpenEye (<a href="http://eyesopen.com/" target="_blank">http://eyesopen.com/</a>) 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). <a href="http://molinspiration.com" target="_blank">molinspiration.com</a> is free to academics and has a tool to break up molecules into fragments, which is a useful underlying technology for scaffold hopping.<br>
<br>
Of course, none of these programs works directly with DOCK - I interpreted your "can be used along with" liberally.<br>
<br>
John<br>
UCSF DOCK Team<br>
<br>
<br>
Dong Xu wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
Hi Dock fans,<br>
<br>
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.<br>
<br>
Thanks!<br>
<br>
-DX<br></div></div>
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