[Dock-fans] Unbiased docking

Scott Brozell sbrozell at scripps.edu
Fri Sep 28 12:42:26 PDT 2007


Hi,

On Fri, 28 Sep 2007, Francesco Pietra wrote:

> Although not yet ready with DOCK6.1 installation, inspection of tutorials
> prompts a couple of questions that may help planning.
>
> What I want to do at the moment is verifying if there is docking at all between
> a family of natural products and a complicated protein. Not in a bilayer for
> the moment.
>
> I have already carried out a conformational search for my natural products by
> simulated annealing with an algorithm that calls Amber9. Parameter and
> coordinate files for Amber9 were built with Antechamber/Divcon (ie AM1).
>
> The tutorial on DOCK web site starts from a protein-ligand complex, ie from a
> definite receptor site in the protein. Is any graphical or alphanumeric
> tutorial for the unbiased docking I am aimed at?

Not that I am aware of.
There is a lot of flexibility in binding sites selection;
see step 3 of
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
If your complicated protein is big then that may put a practical limit
on the size of your grid; one approach would be to divide and conquer
the big protein binding sites into subsets that would be processed
separately.
Perhaps others have comments ?

> DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux amd64 with
> 4GB RAM per cpu, ie a machine better suited for ab initio calculations than
> classical MD), where also Amber9 is installed. Although the X system exists (in
> fact, xleap requires it) and even Gnome could be called, the machine is
> normally used with X killed. I manage anything graphical for Amber9 (to the
> exception of xleap) on a single-Athlon desktop (Debian Linux i386 etch). The
> two machines are scp linked, which is the way I exchange files between the two
> machines.
>
> At 32bit I (1) prepare pdb files for "small molecules" with a MM package; (2)
> examine everything graphical with VMD.
>
> On these basis, where to install Chimera for DOCK? I noticed that Chimera calls
> both Dock Prep and Antechamber.


Installing Chimera on the same machine as VMD seems reasonable.
Any textual input and output files can be communicated between the machines.

> Similarly, where to install dms for DOCK?

dms is small.  I install it in my dock directory.


> I understand that these are generic question, normally not for mailing lists.
> Though, a couple of suggestions would greatly help me (an organic chemist, just
> now beginning to touch the area of the biochemist) in the high complexity of
> the docking affairs.


This is the best place for all questions.

Scott



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