ADL: Docking a drug molecule to a polymer or a crystal surface

surasak chunsrivirot fa833 at
Mon Feb 18 12:33:34 PST 2008


am a newbie to docking softwares and have the following questions. Usually,
Autodock is used for docking of ligands onto receptors. I’m wondering if this
software can be used to blindly dock and calculate the binding energy of the
system of amorphous polymers and a drug molecule or a crystal surface and a
drug molecule? 


anyone knows of any references that use autodock to perform these kinds of
calculations, I would appreciate if you could let me know. I tried to search
for papers that did these but couldn’t find any. I found only papers that use
Biodock (not autodock) to dock and calculate binding scores of a drug molecule
to a polymer though.


people who have used Biodock, is it safe to say that Autodock outperform
Biodock in everyway (speed, accuracy, etc.)? Is this why you switch from
Biodock to Autodock?


you very much for your help.


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