[Dock-fans] DOCK 5.3 runtimes

[Bharat Sukhwani]

Hi,

I recently downloaded DOCK 5.3 and was running the demo on Window's XP.
The demo takes 5 minutes for grid generation and only 15 seconds for 
actual docking. Is this realistic?

I have two specific questions:

1. Is the grid generation step repeated for each ligand or is done only 
once per receptor and the resulting grid/spheres are used across 
different ligands from the database?

2. The ligand mol2 file used in the demo contains only 20 atoms and it 
takes only 15 seconds to dock (out of which, most of the time is spent 
in minimizing the final structure and virtually no time in ligand 
docking (clique identification etc.) itself). Is this typical for 
realistic ligands (i.e. do the have only 20 atoms and take only 15 
seconds to perform docking) ?

I would appreciate if you could provide some insight into this since I 
am interested in the algorithmic complexity of different steps.

Thanks