[Dock-fans] docking protocol

[Jerry Parks]

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