[Dock-fans] dock6 anion false hits

John J. Irwin jji at cgl.ucsf.edu
Thu Feb 28 11:33:42 PST 2008


Hi Hong

Here's what you can always do, for any binding site.

1. Do you have any positive or negative controls? If so, can you 
recapituate what you already know with your docking model?

2. What is the net charge in the binding site? On the whole protein? 
What is the value of the electrostatic potential grid in the binding 
site? Scan you get an atomic decomposition of the score to investigate 
how the molecule got the score it did? Do all the scores (at the atomic 
level) look sensible?

Well, there's more, but this should get you started. Your motto could be 
"Trust nothing, verify everything".

Good luck!

John


Hong Liang wrote:
> Hi Dock Fans,
>
> I do not understand why Dock6 gave me so many anion hits: false hits.
>
> I prepared the acceptor from sybyl 7.3 (adding hydrogens, applied 
> kollman_all charge, manually modified the HIS around binding site to 
> their  neutral state.)  I can not see any  positive charged  residues  
> around the binding site.  After I docked NCI  compounds  downloaded  
> from ZINC website, most of compounds in the top 500 hits are anions.   
> Based on the biology test results of some of the anion hits,  those 
> hits are false ones.
>
> The acceptor prepared by Chimera "Dock Prep" tool gave similar docking 
> result: most of hits are anions.  Did I miss something when I prepared 
> my grid?  Any feedback is appreciate.
>
> Thanks,
>
> Hong Liang
> University of Manitoba
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>
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