Reply To: flexpep docking, select the decoy to do the further docking, questions

[Anonymous]

Dear Michael,
The number of structures to create, lowres pre-optimization and, iterative docking (re-doing docking on the top x decoys) all depend on your system, and your estimate on how close your initial structure is to the native.
In our original benchmark, we do: 100 models with -lowres_preoptimize, and 100 w/o, and select the top 10 and that’s it – i.e. no further refinement (by the way, indeed sorting according to the score is the way to go) You do not need to dock these 10 again, however, we did show that re-docking these shows modest improvement. So basically it’s a question of how much time do you have.
Re. -lowres_preoptimize, this is but a step in the overall protocol followed by high resolution refinement in full-atom mode, so the models you have are still full-atom even if you used this flag. The main difference between running with and without this flag is the possible range of sampling, with the flag you are sometimes able to sample for divergent conformations.

Is it clearer now?
Cheers,
Nir.