[Dock-fans] Docking to Amber Correlation

Scott Brozell sbrozell at rci.rutgers.edu
Wed Jun 18 13:56:30 PDT 2014


On Wed, Jun 18, 2014 at 05:14:15PM +0000, Daniel Graham wrote:
>     I am currently using the dock input parameters shown on the Rizzo tutorial, http://ringo.ams.sunysb.edu/index.php/2014_DOCK_tutorial_with_HIV_Protease .
>     I am currently participating in a docking study where we are using high throughput screening. I am screening millions of compounds using dock6's grid score function, however it yields too many hits to be useful. Is there a way I can be more selective?

There are many approaches; see below for one. 
I'll let the tutorial writers make specific suggestions on their inputs.

>     ?We are also using Amber to perform detailed studies on molecules that show good potential, however some of my top dock scorers (-90 grid score) do not score as well as some of my average scorers (-40 grid score). It seems that after a molecule scores below -30 it might have potential. This presents an issue because Amber calculations take much longer and I don't want to have to go though thousands of compounds basically guessing about which ones may score well in Amber. Is there a way to generate grid scores that better reflect how the molecule will do in Amber?

The general behavior that you state is typical.
One step between Dock grid score and full MD in Amber would be 
Dock Amber score which is MM-GB/SA rescoring.
The default input parameters for Dock Amber score could provide
enough Amber minimization and MD to allow a superior ligand screen
at a computational expense substantially more than grid score
but substantially less than full MD.

There are many caveats, but one important point is receptor preparation.
If i infer correctly that you have already fully prepared your receptor
for your full MD Amber calculations then you may have taken a big step
towards eliminating one source of error in Dock Amber score.
In addition, if you have specific knowledge about the receptor then a
non-default input file using the NAB atom expression could be useful.

For details see


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