[Dock-fans] docking protocol

[John J. Irwin]

Hi Jerry

You might want to contact the authors of that paper at U Maryland for 
advice.

John


Jerry Parks wrote:
> Hello
>
> I'm interested in performing normalized vdW attractive energy scoring as
> described in J. Med. Chem. 2005, 48, 4586-4595. Can Dock 6.2 do this
> automatically, or should I just write a script to extract the vdW
> attractive energy from the output and normalize it myself?
>
> Could you comment on the energy cutoff distance in grid.in? Is it
> reasonable to use a finite cutoff (rather than the 9999 used in the
> tutorial). Is there any general rule for selecting the cutoff besides
> systematically testing the convergence for various cutoff distances? How
> about max_orientations?
>
> Also, is there any sort of general guideline for choosing the "right"
> number of spheres? My binding site is defined by three residues that are
> known to be important from mutation studies. I selected spheres within 8
> Angstroms of those three residues, and then augmented those with
> additional spheres corresponding to xray waters in roughly the same
> region. There are a total of about 40 spheres, and the coverage of the
> binding pocket looks fairly complete to me. Does this sound sufficient?
> Could this be too many spheres?
>
> Thanks,
> Jerry
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>