Knime 2.12, LigPrep/Maestro 2016.3, smina (Apr. 2, 2016)
smina --autobox_ligand on crystal ligand
Test set ligands were prepared using Schrodinger's LigPrep utility.
All inhibitor bound FXR structures were obtained from the PDB and aligned to the provided apo crystal structure.
Only aligned chains to the provided structure were retained (not other chains in the asym. unit). These were removed manually in Maestro.
The receptor (with water) and ligand were split using Schrodinger's tools.
Each test set compound was docked using smina with default parameters to the binding site of three chosen reference PDB structures (3OMM, 3OKH, 3DCU) (102 X 3 dockings).
The 5 top scoring poses for each ligand across docking to the three reference receptors (3 dockings of up to 9 poses) were kept.