Name

quasi-exact

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
AMBER14

Parameter

Default parameters were used for each software.

Method

Compounds were edited into the crystal structure for FXR_10. AMBER force field parameters were then generated for each compound in the set and MD simulations were run for each compound in the FXR_10 receptor. Simulations were analyzed to determine important bond stabilities for each compound. The quasi-exact method as described in https://doi.org/10.1093/bioinformatics/btp664 was then applied to each compound to calculate free energy of binding.

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.