[Blaster-fans] question about targeting specific pockets and subpockets

John Irwin jir322 at gmail.com
Mon Jan 20 07:57:56 PST 2014

Hi Dennis

The pocket picker picks pockets de novo. These are complementary to
whatever pocket you may have specified. You may launch a job to dock to any
of these picked pockets by simply clicking on the corresponding button. You
can also just ignore the pocket picker and proceed with your own job
(below).  I saw that poses and scores were available for the first job #
you sent me.  You can now dock a database (fragments, leads,...) using the
tool starting with "Congratulations! You are now eligible for database

The interface is not very clear for novices. We just fit the pocket picker
in version "1.5" and we still haven't written the paper about it.

Still, it should be usable. Let us know how things go.


On Wed, Jan 15, 2014 at 12:56 PM, Dennis N Bromley <dbromley at uw.edu> wrote:

> Hi all,
> I just had my first successful run on dock blaster and it was very cool.
>  I didn't get exactly the results I wanted, but the software is super
> impressive and I am excited to use it more.
> I am trying to find a ligand that will contact specific residues, so I
> need the pocket specification to be fairly accurate.  My pocket finding
> software (epos ballpass) provides a PDB file with pocket lining atoms
> (basically just a subset of the original pdb file).  So, when I upload to
> dock blaster, I upload the PDB file and this pdb file of pocket-lining
> atoms.  I also set the drop down menu to "binding site residues".
> It thinks for a while and then I get back a list of identified pockets.
>  This is what confuses me because I thought I had just uploaded my pocket
> specification with the pocket-lining pdb file. (?)  Am I doing something
> just dumb here?  I looked at the pockets that it suggested and some of them
> do overlap with mine, but in general they are pretty big and don't zero in
> on the residues that I am trying to hit.
> thanks for any help!  My apologies if this is just a new user question. :)
> -denny-
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