[Dock-fans] Fixing protonation state

John J. Irwin jji at cgl.ucsf.edu
Fri Nov 2 09:49:55 PDT 2007

>> But given the famously high false positive rate of docking, the odds are
>> against you.
> Is any criterion to detect, or suspect (on the basis of DOCK + Amber) false
> positives? 
That would be very useful! I can see how to rule *out* compounds by
coding up the same rules of thumb we use when looking at top scoring
hits (good overall steric, hydrophobic and shape complementarity,
penalize stranded polarity, and missed opportunities in the
protein-ligand complex. But I see this more as "getting rid of junk"
rather than pretending to scrupulously eliminate false positives.


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