[Dock-fans] Fragment screening

John J. Irwin jji at cgl.ucsf.edu
Fri Jun 12 06:56:04 PDT 2009

Hi Chris

Thanks for your email. We use DOCK 3.5.54 for all of the research in our
group, which you may find here:
http://shoichetlab.compbio.ucsf.edu/publications.php.  Thus the papers
you cite below are the rule rather than the exception.   We know of many
people who use DOCK 6.  We just use DOCK 3.5.54 because we developed it
and we know its strengths and weaknesses best.

I hope this helps.


Chris Arthur wrote:
> I'm looking to do some fragment screening, and spent a very entertaining 
> evening last night with
> Molecular docking and ligand specificity in fragment-based inhibitor 
> discovery
> Nature Chemical Biology 5, 358 - 364 (2009)
> and
> Docking for fragment inhibitors of AmpC β-lactamase
> PNAS May 5, 2009 vol. 106 no. 18 7455-7460
> Both are excellent articles and well worth a read if you haven't already 
> done so.
> Anyway, my dillema. Both of these articles use Dock 3.5. Can any of the 
> list members or authors tell me why 3.5 was used rather than 6 and 
> whether 6 would be up to the job in a similar manner. The closest the 
> papers get to explaining it is to say something along the lines of 3.5 
> uses a simple physics scoring algorithm that doesn't penalize fragments 
> for being, well, fragment like.
> Thanks for any input
> Chris
> _______________________________________________
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> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
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