[Dock-fans] max spheres limit

[Scott Brozell]

Hi,

On Mon, 28 Jan 2008, Ben Keshet wrote:

> Sudipto recently commented about the limitation of the max number of spheres
> being 50-75.  I have found a similar comment about dock5.3:
> http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2005-December/000508
> .html
> 
> Can anyone support or provide any more information about the limitation of
> Dock with large clusters? Is Dock6.1 any better than 5.3 with regard to
> that? Is the limit different for rigid and flexible docking? Is there any
> intelligent way to overcome that limit?  

Yes, DOCK has practical limitations due to available hardware resources.
A series of benchmarks would be useful; I'll see what I can find.
DOCK 6 is much better than DOCK 5 with respect to memory handling
and consumption because of Terry Lang's work.
Flexible docking is more memory intensive than rigid:
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2006-August/000679.html
All approaches for circumventing these kinds of limitations are
based on divide and conquer, and the various common ways of
getting smaller pieces have been mentioned in this list.

> 75 spheres are often too small for my ligands.  I could manually edit the
> SPH file and delete less likely spheres, but I would prefer avoiding such
> speculations.  

For large ligands note that the anchor-and-grow
conformational search algorithm has been validated
for binding mode prediction on sets of ligands that have
no more than seven rotatable bonds:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Moustakasetal2006

Scott

> Date: Fri, 28 Dec 2007 23:17:50 -0800 (PST)
> From: Sudipto Mukherjee <sudmukh at yahoo.com>
> Subject: Re: [Dock-fans] bad allocation
> 
> Dear Barbara,
> 
> Docking works well with about 50-75
> spheres in the binding site. Could you specify how many spheres you are
> using? Are all roughly in the binding site? Selecting more spheres
> would increase the box size for the grid. The size the grid file
> increases roughly as the cube of the box size i.e. proportional to the
> volume of the box.
> 
> I have tested DOCK successfully with grid
> files as large as 800MB on a computer with 2GB RAM . However, if the
> grid file is larger than the amount of available memory, memory
> allocation errors like the one described is likely.