[Dock-fans] Comparing docking strategies

John J. Irwin jji at cgl.ucsf.edu
Mon Apr 28 15:16:37 PDT 2008

Hi Francesco

When evaluating docking procedures and protocols, you should have in 
mind a scientific question (e.g. how does molecule X bind? Can I find 
molecule X from among a sea of decoys?). The second point is to 
calibrate your model by attempting to recapitulate all available binding 
information (e.g. IC50s, crystal structures). Third, the ultimate test 
is the usefulness of the predictions made by docking, which you test by 

Both of your approaches make numerous assumptions and approximations. To 
find out which protocol is "best", I suggest you use each method to make 
predictions, both retrospectively and prospectively, and test them.

Good luck!


Francesco Pietra wrote:
> Can anyone compare the relative merits/deficiencies of the following two docking strategies? (the first one is what I am using with DOCK6)
> (1) Flex-docking followed by amber-score (everything), followed by molecular dynamics of the complex in an as-much-as-possible realistic environment (such as a lipid membrane in the case of a transmembrane protein, or otherwise).
> (2) Simulated annealing procedure (with a different docking program) to explore the binding possibilities of a ligand in a binding pocket, evaluating  the interaction energy of ligand/protein using atom affinity potentials calculated on a grid. All that by allowing to move the ligand atoms only (not those of the receptor).
> This is a purely scientific question, without any aim to compare specific programs. Also, I am prepared to accept that different problems may require different strategies. The comparison should also take into account that I select ligand conformations (to submit to docking) from MD simulated annealing in vacuo.
> Thanks for comments.
> francesco pietra
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