[Dock-fans] Fragment screening

Chris Arthur chris.arthur at bristol.ac.uk
Thu Jun 11 01:54:51 PDT 2009

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 
Nature Chemical Biology 5, 358 - 364 (2009)
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


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