[Dock-fans] how do I choose the scoring functions?

[John J. Irwin]

Hi Yolanda

The short answer is: use the score that best recapitulates what you 
already know. In general, in our experience, this has been van der Waals 
+ electrostatics + desolvation, which are fastest when calculated via 
pre-calculated grids. But like they say at the CIA, you should trust no 
one - you must convince yourself that you are using a scoring function 
that adequately captures the features of the molecules and the binding 
site you are investigating, for instance, well enough to re-dock a known 
ligand and to enrich known actives from among a forest of 
property-matched decoys.

Good luck

John


Äî Áõ wrote:
> Hi,dock-fans
>  
> I have a puzzle in mind. I know that DOCK has several types of scoring 
> functions,but normally,how should I select them?
> I'm a novice in dock and trying to identify some small molecules such 
> as inhibitors by database screening. However,in face of so many types 
> of scoring functions(contact score, grid-based score, amber score 
> etc.), I don't know which one fits my experiment.
> Any help would be appreciated!
> Thanks in advance!
>  
>  
> Best regards,
> Yolanda Guo
>
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