[Dock-fans] Sphere_selector

William Joseph Allen william.joseph.allen at gmail.com
Thu Jul 18 06:45:59 PDT 2013

Hi Mahesh,

You may need to provide a more thorough description of your set up and
docking parameters before we can give a very helpful answer. We don't know
either if what you are getting is right or not, because we don't know
anything about the system, and almost nothing about the set up. Here are
some questions, some of which were already posed, that would let us help
you better:

When you said you used 10 Angstroms in INSPH, what exactly do you mean?  I
think you mean to say you used a 10 Angstrom cutoff in sphere_selector,
which is the following step. How specifically are you selecting a subset of
spheres? What and where are your reference atoms for sphere_selector? When
you selected a subset of spheres, did you open up the resulting file (in a
viewing program like chimera) in the context of the receptor? You should be
able to confirm whether or not the spheres are actually in the binding site
that you are interested in. When you generated a box around the spheres,
what margin did you use? When you open up the box in chimera (along with
the spheres and the receptor), is the binding site fully encompassed? Can
you briefly summarize your docking protocol?

If the spheres are not within the binding site that you are interested in,
and if the box does not fully encompass the binding site, then it is
unreasonable to expect that your ligand will dock successfully. Perhaps it
would be helpful for you to consider the function of spheres during docking
- they serve as starting points for placing small segments (in other words,
the anchor) of your ligand within the binding site that you want to explore.

Joe Allen

On Thu, Jul 18, 2013 at 4:58 AM, Mahesh Hegde
<mahesh at biochem.iisc.ernet.in>wrote:

> Hi everyone..
> Last tome i asked some question about sphere generator, i was not able to
> dock when i used 10 ?ngstr?m (in INSPH), it was not binding in the right
> pocket, but i increased 30 angstrom so that all spheres will get selected,
> and i got some what good result (now its binding in the pocket, slightly
> different manner), i don't know what i am getting is right or not, may i
> get someones help?
> --
> Sincerely,
> Mahesh Hegde
> --
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William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
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