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

John Irwin jir322 at gmail.com
Thu Jan 16 09:09:23 PST 2014


Thanks for your email. I will reply by the weekend.


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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