[Dock-fans] Amber scoring

Scott Brozell sbrozell at scripps.edu
Thu Jul 26 12:56:19 PDT 2007


Hi,

On Wed, 25 Jul 2007, Alessandro Nascimento wrote:

> I would like to know from those who have already achieved good results
> using grid (primary) / amber (secondary) score to search databases
> like zinc: is there any good threshold to be used as an indicative of
> success by amber scoring function?

I would also like to hear answers to this and not just for Amber score.
In my limited experience its all relative.
Here is my usual reference to the errors in docking
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-July/001103.html

Scott

> In dock6 tutorial page there's a graph showing binders and decoys
> using amber score. There, the best binder achieves ~ -17.00 as amber
> score. Would this value be a good indicative?




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