[Dock-fans] Docking to Amber Correlation

Daniel Graham daniel.graham at centre.edu
Wed Jun 18 10:14:15 PDT 2014


    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?

    ?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?

    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 .



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