Reply To: low resolution blind protein-protein docking with a ligand

[Anonymous]

Sorry I don’t have much time to look into this, but here’s a couple thoughts:

– my guess, without looking at the logfiles or scorefiles, is that a docking filter is being tripped up and it is having to re-do the decoys at some stage in the docking algorithm. When I used interfacial ligands, the differences in computational time was negligible because the system size was largely unchanged.

– did you look any of the outputted decoys? Another related explanation could be the fold tree or dock jump is incorrectly specified and the heme is being treated as the second partner, but since its very restricted from translation/rotation movements dock-perturbations are tripping the docking filters and restarting low-res mode.

hope this helps.