# Name for the protocol
Name: Maestro/Omega/MGLTools/Autodock Vina Method 1
#
# All software packages used and their versions:
Software: Maestro/Omega/MGLTools/AutoDock Vina
#
# List of key parameters used for system preparation
System Preparation Parameters: Assumed pH 7.4
System Preparation Parameters: Tautomers considered
System Preparation Parameters: Gasteiger charges
#
# Plain-text description of system preparation method
System Preparation Method: Maestro's prepwizard was used to add hydrogens using default parameters.  
All the waters were retained while GAFF force field parameters were assigned to the protein and all 
ligands. The binding site residues, which were considered to be residues 56, 65, 200 and 210, were energy minimized. 
Ligand conformational libraries were generated using OMEGA. The most stable 
conformation found for each ligand was then used as a starting point for docking. 
Preparation for docking with Vina was done using MGLTools where the ligand PDB files from 
OMEGA were converted to PDBQTs by assigning charges and atom types. The binding site residues
above were treated as flexible and the grid box determined.
#
# List any number of key computational parameters in the following lines:
Pose Prediction Parameters: Iterated Local Search global optimizer search method
Pose Prediction Parameters: Exhaustiveness=50 #exhaustiveness of global search (default=8)
Pose Prediction Parameters: Vina scoring funtion (empirical + knowledge-based function)
Pose Prediction Parameters: Num_modes=5       #max number of poses to generate
Pose Prediction Parameters: Energy_range=5    #energy difference (kcal/mol) between the best and worst binding mode
#
# Provide free text description of your method below. Use as many lines as you need. 
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 5 poses from the Vina docking are submitted with this protocol. 
#
# Yes/No questions:
# Question 1: Did you use visual inspection to select, eliminate and/or manually adjust your final predicted poses?
# Question 2: Did you use publicly available co-crystal structures of this protein with similar ligands to guide your pose predictions?
#
Answer 1: Yes
Answer 2: Yes