[Dock-fans] Comparing docking strategies

Francesco Pietra chiendarret at yahoo.com
Sun Apr 27 10:33:12 PDT 2008

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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