[Dock-fans] contact score or energy score,which is reliable

John Irwin jji at cgl.ucsf.edu
Tue Apr 26 09:07:15 PDT 2005


Hi Sudheer

Thanks for your question about DOCK scoring. For small molecule docking, in
my experience you want the energy score. The only time we have use the
contact score in recent years has been for protein-protein docking, for
which the energy score was too noisy. If you are not getting the orientation
you think you should get, you need to work backwards through the ligand
preparation, the receptor preparation and the docking parameter choices to
investigate why.

Hope this helps.

John

> -----Original Message-----
> From: dock-fans-bounces at docking.org 
> [mailto:dock-fans-bounces at docking.org] On Behalf Of sudheer karanam
> Sent: Friday, April 22, 2005 3:18 AM
> To: dock-fans at docking.org
> Subject: [Dock-fans] contact score or energy score,which is reliable
> 
> hai,
>  i've used dock for knowing binding mode of ligand into 
> receptor.first i used both contact score and energy 
> score.then i used only energy score.both the runs have given 
> different orientation of the ligand into the receptor.which 
> one i should take into consideration.which is more reliable 
> mode of binding.please help.thanking you in advance...sudheer 
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