[Dock-fans] Comparing docking strategies
John J. Irwin
jji at cgl.ucsf.edu
Mon Apr 28 15:16:37 PDT 2008
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.
UCSF DOCK Team
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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