[Dock-fans] grid parallelization?

Scott Brozell sbrozell at scripps.edu
Tue Nov 13 22:06:39 PST 2007


On Tue, 13 Nov 2007, Francesco Pietra wrote:

> I wonder whether the calculation of grid is suitable to parallelization in a
> future version of DOCK.
> Using Magis' sphgen_cpp I can treat a whole pore protein model. I recognized
> today that I has spheres for only a portion of the protein. Therefore, using
> Magis' sphere_select, I have now selected a radius around a central atom within
> the pore (the oxygen of a "natural" HOH residue). Because I am exploring
> without previous knowledge where the ligand prefers to dock, I am creating a
> grid for a box measuring 66 66 66 A for a total of more than 10 millions
> points. In 30 min 10% of protein atoms processed. All processors, except one
> (100%) are dormant.
> That of having a point of symmetry is another problem. Luckily I had that
> oxygen of WAT residue in the receptor noH.pdb file.

Thanks for the suggestion; we'll add it to the list.
However, the flip side is that really big grids have to be stored and
then read by program dock.  The divide and conquer approach suggested in
the tutorials is tractable and amenable to very coarse grained
parallelization for both grid and dock, ie parallel runs of grid and dock. 
An alternative in the era of the approaching petascale computing
is gridless DOCKing.


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