ADL: Docking inside recptor (David Crosby)

Antonio Cavazzuti acavazzuti at
Mon Mar 17 09:51:40 PDT 2008

Hi David, 
did you solved the problem concerning the docking inside the receptor?
(problem reported in autodock Digest, Vol 48, Issue 17)
If yes, can you suggest me how to avoid this problem?
Thank you!

> 1)       I've noticed often when I attempt to dock a ligand I'll get 
> a handful (perhaps 5 in 25-50) of dockings where the ligand is 
> docked quite literally inside the macromolecule resulting in some 
> astronomical dG value. Is there some setting I'm missing when I set 
> up my grids or docking parameters to tell Autodock to avoid 
> nonsensical dockings?  I see you can specify an upper energy limit 
> under the docking parameters menu, but can I assign a lower limit to 
> avoid these wild results?  They throw off the clustering data.  I'm 
> attempting to dock a somewhat small molecule with 4-6 torsions onto 
> a relatively small receptor (~6kd,)  I'm trying to keep my initial 
> dockings unbiased, so my grid envelops the entire receptor. I've 
> left plenty of space for the ligand to rotate freely in all 
> configurations, so why does my ligand often end up inside my 
> receptor instead of on the surface?  I understand autodock first 
> introduce 50 randomly placed/oriented ligands inside the grid volume 
> and make calculations from there, but why would it consider 
> molecules making obviously high-energy (or low) contacts with other 
> atoms as preferable dockings?

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