[Dock-fans] DNA-LIGAND docking

[Scott Brozell]

Hi,

On Fri, 20 Mar 2009, Sarathbabu K wrote:

>            Can any one please send me the procedure for doing the
> DNA-LIGAND docking using the DOCK 6.2 tool..i am not able to understand the
> tutorial given in the website.moreover the tutorial explains the docking
> procedure for a protein and i need to dock with a DNA.So please help me out.

In principle the protein-ligand tutorials cover DNA-ligand DOCKing.
Many have used the tutorials; what is unclear ?
I suggest all 5 tutorials
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
since Amber score may be useful for DNA flexibility.

Scott