# Name for the protocol
Name: dock_close
#
# All software packages used and their versions:
Software: Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Software: Openbabel 2.3.2
Software: Pymol 1.7.4.5 edu
Software: Omega2 2.5.1.4
Software: Python 2.7.11
Software: Matplotlib 1.5.1
Software: Scipy 0.17.0
Software: Click 6.6
#
# List of key parameters used for system preparation
System Preparation Parameters: Default parameters used for all programs.
#
# Plain-text description of system preparation method
System Preparation Method: Publically available holo structures of FXR were obtained from the pdb and then aligned to the apo FXR structure provided.
#
# List any number of key computational parameters in the following lines:
Pose Prediction Parameters: Default parameters used for all programs.
#
# Provide free text description of your method below. Use as many lines as you need. 
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.
