[Dock-fans] Fatal error about amber score.

John J. Irwin jji at cgl.ucsf.edu
Tue Apr 15 10:45:08 PDT 2008

Hi -

DOCK as used for virtual screening is a program to prioritize compounds 
for purchase and experimental testing. We know from experience (and it 
is well attested in the literature) that most top scoring compounds 
generally do not bind. This is easy to explain: many approximations are 
made in the docking calculation. You can make a case that docking, in 
general, should not work.

Any calculated value should not be trusted, but instead used for 
purchasing guidance. Look at docking as a way to identify compounds to 
test in the lab. If we buy 50 compounds hand picked from among the top 
500, and 3 of them bind to the protein, we are thrilled.

Good luck


Sivakumar subramaniam wrote:
> Dear fans,
> help me ,
> there any factor in dock that will give the inhibiting level of the 
> protein with the ligand used. In some tool its is said to be the RMSD 
> value, but when i calculated the RMSD value, it does int show any 
> indication about the inhibiting level. is there any other parameter to 
> calculate the inhibition value.
> s.sivakumar
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