[Dock-fans] How to dock in protein which doesn't have reference internal ligand

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jul 19 11:18:01 PDT 2011


Hi,

On Tue, Jul 19, 2011 at 08:48:06PM +0530, diya singh wrote:
> 
> I have learned the basics of DOCK6. I am trying to figure out how should I
> go ahead in docking procedure if my PDB protein doesn't have internal
> ligand. When I tried using my external molecule as ligand. Sphgen command
> results 0 spheres.
> 
> How should I dock in such kind of protein.
 
If you are referring to blind docking then search the list for it:
http://dock.compbio.ucsf.edu/DOCK_6/index.htm#searchdockfans
Here are some good hits:
http://mailman.docking.org/pipermail/dock-fans/2007-November/001328.html
http://mailman.docking.org/pipermail/dock-fans/2007-December/001337.html
http://mailman.docking.org/pipermail/dock-fans/2007-December/001340.html

http://mailman.docking.org/pipermail/dock-fans/2011-January/002458.html
...
http://mailman.docking.org/pipermail/dock-fans/2011-January/002471.html

good luck,
scott



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