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

Dennis N Bromley dbromley at uw.edu
Wed Jan 15 12:56:35 PST 2014

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. :)
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