ADL: How to make a flexible chain staying in the active pocket

Jun-Wei zhaojunwei2004 at 126.com
Thu Apr 2 00:40:36 PDT 2009


Dear AutoDockers,
 
I'm trying to dock a ligand to a metalloenzyme containing zinc ion by AutoDock4. The zinc is in the active pocket of the protein. My ligand has a sidechain containing five C-C single bonds, which should be located in the active pocket theoretically.
  The question: when checking the docking results, all the docked poses bind to the protein surface around the pocket, instead of binding into the zinc pocket with the five C-C single bonds. What should I do to get the sidechain into the pocket? Thanks in advance!
 
  The grid box is properly set around the pocket and different zinc parameters have been tried.

Best wishes,
Junwei Zhao


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