[Dock-fans] Need help!

[John J. Irwin]

Hi Yolanda

Do you have any controls against which to test your docking 
parameterization? If you do (crystal structures are best, but confirmed 
reversible, competitive, non-covalent IC50s or Kis will do) then dock 
them and check that they score well, and pose reasonably. Second, dock 
some other molecules with similar physical properties (mwt, logP) and 
make sure the ligands score better than most of these "decoys" - if they 
don't, then you're not going to be able to pull known actives out of a 
screening deck.

Once you have passed these two tests, you are ready to move on to 
docking a database. If you don't have any controls, then, if the 
molecules you docked looks plausible, buy them and test them. What you 
want more than anything else is experimental hits. Once you have those, 
you can tune your scoring function and docking parameterization to them, 
so you can find more hits, and so on.

Good luck!

John



Äî Áõ wrote:
> Dear Dock-fans:
>  
> I think I need help.
> Not long ago, I studied the small molecule virtual screening with 
> dock6.Recently, I obtained top 1500(about 50% of total compounds) 
> scored compouds from database.In my docking,I set the grid score and 
> contact score.In the result files,the compounds were sorted by the 
> grid score.
> Now the problem is what should I do next. How do I treat these compouds.
> Should I rescore these 1500 compouds with Amber score? Or I should use 
> some other programs to proceed,I don't know .
> This problem has troubled me for a long time.I 'm expecting any 
> suggestions.
> Any help would be much appreciated.
>  
>  
> Best regards,
> Yolanda Guo
>
> ------------------------------------------------------------------------
> Looking for last minute shopping deals? Find them fast with Yahoo! 
> Search. 
> <http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping> 
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>