Knime 2.12, LigPrep/Maestro/IFD/Desmond 2016.3, Binding pose metadynamics 2016.4, smina (Apr 2. 2016)

System Preparation Parameters


System Preparation Method

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.

Pose Prediction Parameters

Poses to generate 20
Refine residues within 5.0 A
Glide SP redocking
Binding site defined by co-crystal ligand
Receptor vdW scaling 0.50
Receptor vdW scaling 0.50
Auto box size

Pose Prediction Method

For each test set compound, poses were manually selected based on their similarity to known crystal poses, contacts with the protein and similarity to other predicted poses.
As these poses come from a variety of methods, the scores associated with them are arbitrary.