# Name for the protocol
Name: Maestro/Marvisketch/rDock Visual
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# All software packages used and their versions:
Software: Maestro 11 (Beta Version)/ fconv/ Open Source Pymol 1.7 /MarvinSketch 15.3.30/ rDock
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# List of key parameters used for system preparation
System Preparation Parameters: Assumed pH 7.4
System Preparation Parameters: Tautomers considered
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# Plain-text description of system preparation method
System Preparation Method: Maestro's prepwizard was used to add hydrogens using default parameters.
The FXR structure provided by the organizers was used as initial template.
The structure was converted to mol2 files using fconv for the docking calculations, after initial cleaning with Maestro.
For the alchemical free energy calculations it was necessary to model a missing fragment comprised of residues A459-K464.
To this end the protein residues between N448 and Q476 were replaced by the same fragment as crystallized in the 3OKH structure. Subsequently, ACE capping groups were added to residues M247 of the main chain and D743 of the co-activator fragment.
Similarly an NME capping group was attached to D755 of the co activator fragment.
Ligand 3D structures were generated from 2D sdf files provided using MarvinTools scripts.
No water molecules were retained for docking calculations.
For the alchemical free energy calculations coordinates for water molecules accompanying the X-ray structure provided by
the organisers were superimposed with the coordinates of the poses. It was found that 1 water molecule
was susceptible of interfering with the simulations of the largest compounds (such as fxr_102). Consequently it was manually displaced to a nearby position.
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# List any number of key computational parameters in the following lines:
Pose Prediction Parameters: RECEPTOR_FLEX 3.0 # Receptor flexibility weight
Pose Prediction Parameters: SITE_MAPPER RbtSphereSiteMapper # Cavity definition function
Pose Prediction Parameters: SMALL_SPHERE 1.5 # Small sphere radius for the cavity mapper
Pose Prediction Parameters: LARGE_SPHERE 4.0 # Large sphere radius for the cavity mapper
Pose Prediction Parameters: SCORING_FUNCTION RbtCavityGridSF     #Cavity scoring function
Pose Prediction Parameters: WEIGHT 2 # Pharmacophoric restraint penalty weight
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# Provide free text description of your method below. Use as many lines as you need.
Pose Prediction Method: Docking calculations were performed for compounds fxr_91, fxr_101 and fxr_102. Docking was performed with rDock, generating the cavity using the two sphere method available in the program, centering a 15 A cavity within residues M294, I356, S336 and Y373 using 1.5 and 4.0 A for the radius of small and large spheres respectively. As pharmacophoric restraint an aromatic ring was forced within 4 A of the the center of the cavity.
Coincident binding modes were obtained for the 3 compounds. However, to minimize the differences between binding modes of the different compounds, poses for the 17 compounds in the set were derived from a common scaffold.
To this end, the BM of the largest compound FXR_102 was selected as a template and subsequently modified in Maestro to obtain poses that were minimized using the internal forcefield to avoid steric clashes.
