p2wkt-LigandScoringProtocol.txt

Name

Maestro/ChemScore

Software

Maestro 10.2/AutoDock Vina 1.2/Sybyl 2.1

Parameters

XP precision docking with post minimization

Method

For first 36 molecules the x-ray structures were used for scoring and docking was not perfermored on them.For other molecles a receptor (1kjyp-AA) was selected based on the results of a cross-docking study. Receptor was prepared by Maestro's prepwizard and energy minimized. Ligands 3D-conformation were minimized using Ligprep. The results was rescored by Chemscore as it outperformed other tested scoring functions in a priliminary study conducted on a set of FXR agonists with known activity.

p2wkt-PosePredictionProtocol.txt

Name

cross-docker/Maestro

Software

Maestro 10.2/AutoDock Vina 1.2/Sybyl 2.1

System Preparation Parameters

Default setting of Protein Preparation Wizard of Maestro
Ligands were prepared using ligprep

System Preparation Method

For first 36 molecules the x-ray structures were used for scoring and docking was not perfermored on them.For other molecles a receptor (1kjyp-AA) was selected based on the results of a cross-docking study. The receptor was prepared by Maestro's prepwizard and energy minimized. Ligands 3D-conformation were minimized using Ligprep.

Pose Prediction Parameters

XP precision docking with post minimization

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. The top 1 pose from the Glide docking for each ligand was submitted for rescoring by ChemScore.