[Blaster-fans] Does DockBlaster identify mostly internal cavities?

John Irwin jir322 at gmail.com
Wed Dec 18 09:49:10 PST 2013


The algorithm is not currently good at finding buried pockets. These should
be pretty obvious, so just tell the program where you want do dock by
supplying the residues that make up the binding site.


On Wed, Dec 18, 2013 at 9:38 AM, Dennis N Bromley <dbromley at uw.edu> wrote:

> Hi everyone!
>
> I recently uploaded a protein structure to DockBlaster with a known
> internal pocket, maybe 400- 500 cubic angstroms.  The pocket opens up to
> the surface, but the majority of the surface area is internal.  I have also
> docked a ZINC ligand into the pocket using AutoDock VINA.
>
> When I submitted the protein structure to DockBlaster, it accepted the
> protein PDB without error, but then later errored out saying that there
> were no pockets.  It still did this even when I uploaded the VINA-docked
> ligand with it.
>
> Am I doing something wrong or does the DockBlaster pocket finding not like
> mostly internal pockets?  I apologize if this has been dealt with earlier,
> but I was not able to find any previous similar discussions.
>
> thanks and happy holidays!
> -denny-
>
>
>
>
>
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>
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