0pgek-LigandScoringProtocol.txt

Name

align_manual

Software

Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.7.4.5 edu
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6

Parameters

Default parameters used for all programs.

Method

Aligned poses were compared to compounds in free energy prediction sets and ranked manually.

0pgek-PosePredictionProtocol.txt

Name

dock_close

Software

Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.7.4.5 edu
Omega2 2.5.1.4
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6

System Preparation Parameters

Default parameters used for all programs.

System Preparation Method

Publically available holo structures of FXR were obtained from the pdb and then aligned to the apo FXR structure provided.

Pose Prediction Parameters

Default parameters used for all programs.

Pose Prediction Method

For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then docked to the corresponding receptor structure with docking box defined by the cocrystal ligand. The best pose or poses were then selected by hand from highest scored poses.