[Dock-fans] Which one I use in DOCK

Scott Brozell sbrozell at scripps.edu
Fri Feb 1 17:01:02 PST 2008


Hi,

On Fri, 1 Feb 2008, snoze pa wrote:

>  I am trying to use DOCK for screening a list of ligand. I am using
> following tutorial
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
>
> 1.Rigid and Flexible Ligand Docking and AMBER Score are different or  both
> are part of the dock process.
> 2. If no, then which one is better
>
> Is not clear from website which one perform better than other.

Rigid and Flexible Ligand Docking and AMBER Score are different
because currently Amber score can only be used for rescoring poses,
not for generating poses.
In general, the dock process would include all five of the tutorials
performed in the order they are listed at the web site,
perhaps rescoring with a different score than Amber score.

Scott




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