[Dock-fans] Fragment screening

Suxin Zheng sxzheng at u.washington.edu
Thu Jun 11 17:35:29 PDT 2009


I also wonder if they have compared the scoring rank and conformation  
derived from the dock3.5 and dock6.

On Jun 11, 2009, at 1:54 AM, 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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-----------------------------------------------------------------
Suxin Zheng
Research Associate, Varani Group
Box 351700
Department of Chemistry, University of Washington
Seattle, WA, 98195-1700
Tel: 206-543-5081
sxzheng at u.washington.edu




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