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

Dennis N Bromley dbromley at uw.edu
Wed Dec 18 09:38:05 PST 2013

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!
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