[Dock-fans] Fragment screening

John J. Irwin jji at cgl.ucsf.edu
Fri Jun 12 06:57:07 PDT 2009


Hi -


Suxin Zheng wrote:
> I also wonder if they have compared the scoring rank and conformation
> derived from the dock3.5 and dock6.
No, we did not do this.  We have done so in other studies, but not in
this one.

John
>  
> 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 <mailto:sxzheng at u.washington.edu>
>
>
>
>
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