[Dock-fans] DOCK 5.3 runtimes

[John J. Irwin]

Hi

Bharat Sukhwani wrote:
> 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?
>   
sounds about right to me
> 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?
>   
b. only once. that's the whole point of grids.
> 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) ?
>   
yes. minimization, depending on how it is done, can increase time per
molecule by a factor of 10, or even 100.
> I would appreciate if you could provide some insight into this since I 
> am interested in the algorithmic complexity of different steps.
>   
this is a pretty well studied subject, although perhaps not formally in
the computer science sense.  To do this properly you really need to
start by reading the literature to see what has already been done, and
then formulate your question.  What exactly do you want to know, and
what is your motivation?
 
It is unclear exactly which version of DOCK you are referring to. 5.3 is
obsolete. Do you mean 5.4 (also obsolete), 6.2, or 3.5?
> Thanks
>
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