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

John Irwin jir322 at gmail.com
Wed Dec 18 09:47:52 PST 2013

The pocket picker has important limitations. If you send me the job number
or the PDB file itself, I can take a look and at least give you an opinion.
 The pocket picker is supposed to make your life easier, but there is no
substitute for taking a good look yourself.  You are looking for an
invagination that has substantial grease, but at least a couple of polar
handles. For an example of platonic binding sites, take a look at the many
recent small molecule binding GPCR structures in the PDB.

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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