Name

dock_cross_1OSV

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

Each test compound was docked using smina to the receptor of 1OSV with waters removed. The best affinity score estimate for each compound was used to generate its ranking.

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.