A short write-up of the workflow I used to predict binding poses of PXR (pregnane X receptor) ligands by molecular docking.

Method

  • Software: UCSF DOCK.
  • Receptor structure: PDB entry 8SVX, used as the docking target.
  • Grids: generated with the standard settings – no optimization or hand-tuning of the scoring grids was performed.
  • Ligand preparation: the standard UCSF DOCK ligand building pipeline was followed to construct and prepare the ligands for docking.
  • Geometry fixes: two ligand structures failed validation in the building pipeline. These two were re-optimized with MOPAC at the PM7 semi-empirical level before being passed back into the docking workflow.

This is a deliberately lightweight setup – default grids and the out-of-the-box ligand pipeline – intended as a first pass at the binding poses rather than a finely tuned protocol.