[Blaster-fans] question about targeting specific pockets and subpockets
Dennis N Bromley
dbromley at uw.edu
Wed Jan 15 12:56:35 PST 2014
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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