FBRHGRM Method 1


Open Babel 2.3.2/UCSF Chimera, alpha version 1.11 (build 40585)/GROMACS 5.0.2/MODELLER 9.14/Surflex-Sim 2.745/AutoDock Vina 1.1.2/Clusterizer 1.0/DockAccessor 1.0

System Preparation Parameters

Crystallization pH #used to derive each published co-crystal structure (for the minimization process)
AMBER ff99SB-ILDN charges #for the minimization process of published co-crystal structure
Crystallization pH #used to derive each D3R co-crystal structure (for the docking simulations)
Gasteiger charges #for the docking simulations of D3R ligands

System Preparation Method

For preparing the locks, all the human FXR co-crystal structures available from the Protein Data Bank
have been downloaded and cleaned (removal of water molecules, etc..).
The non-terminal missing residues were rebuilt using MODELLER 9.14 while maintaining the experimentally-determined portion fixed;
for each complex, 50 models were built and the structure with the lowest DOPE score was selected.
The obtained complexes have been protonated according to each relative crystallization pH (different co-crystals have been crystallized
at different pH) and energetically minimized in a water box using the GROMACS 5.0.2 program with the AMBER99SB-ILDN force field.
All the water molecules were removed after the minimization.
The minimized proteins have been isolated from the relative co-crystallized ligands and used as locks to perform a subsequent ensemble docking.
3D PDB structures of the provided D3R compounds have been obtained using the Open Babel suite, protonated at the relative crystallization pH
and pre-aligned to the experimentally resolved FXR agonists (available from the Protein Data Bank website, using Surflex-Sim) to generate
an improved starting point for the ensemble docking.
MGLTools was used to convert PDBs into PDBQTs. The grid box was determined according to the crystallized keys and D3R's FXR ligands.

Pose Prediction Parameters

A.starting_model = 1 #index of the first model for MODELLER
A.ending_model = 50 #index of the last model for MODELLER
Integrator = steep #algorithm (steep = steepest descent minimization) for GROMACS
Emtol = 1000.0 #stop minimization when the maximum force < 10.0 kJ/mol for GROMACS
Nsteps = 5000 #maximum number of (minimization) steps to perform for GROMACS
Exhaustiveness =100 #exhaustiveness of global search for AutoDock Vina
Vina scoring function
Num_modes = 20 #max number of poses to generate for AutoDock Vina
Energy_range = 10 #energy difference (kcal/mol) between the best and worst binding mode for AutoDock Vina

Pose Prediction Method

Docking runs were executed with the above specified parameters.
The Clusterizer & DockAccessor programs have been used to extrapolate the lowest energy (D3R)ligand-protein conformations.
The top (lowest energy) poses from the Vina docking is submitted with this protocol.