MMGBSA ranking from 20 MD replicates
AMBER14
Assumed pH 7.4
1. Starting structure: Protein PDB files were prepared by using Glide XP Docking approach with the AB chain in 1KJYP for the FEP18 data set(AA Chain for FXR_12, FXR_38, FXR_41).
2. MD simulation: Use AMBER14 to equilibrate the protein-ligand complex starting structure for 5 ns, then run additional 20 replicates with 5ns each by restarting from the identical equilibrated atomic coordinates but different initial velocities generated from a Maxwell-Boltzmann distribution.
3. Ranking Score: The last 1.5 ns of each replicate was used as the production, which generated 300 snapshots in total. AMBER MMGBSA method was used to analyze the total free energy. Entropy contribution was not included.
Glide
Schrodinger software used: glide version 72015 (mmshare version 35015) used for grid building and ligand docking, prepwizard utility for protein preparation, ligprep for ligand preparation,python version: 54015 for ligprep, prepwizard utilities
Assumed pH 7.4
Starting structure: Ligands were prepared using Schrodinger's standard ligand preparation at pH 7.4. The stereochemistries were given in the isosmiles strings and were therefore kept. Proteins were prepared using Schrödinger.s protein preparation wizard. Bond orders were assigned, hydrogen atoms added, disulfide bonds were generated, and water orientations were sampled. The charge states were kept at pH 7.0. Missing loops and side chains were constructed. The given residue confirmations were kept, with no alternative residue conformations examined.
no waters considered
Automated Ensemble Docking approach using all structures available in the PDB.
All PDB chains overlayed into reference apo structure.
Proteins and ligands prepared with Schrodinger software.
Preparation of docking grids
- use protein chains overlayed and prepared as above
- define cubical grid box that contains all ligands in x-ray structure
- calculate all grids using same box and mostly default parameters
- no waters considered
Ensemble docking workflow:
- dock each ligand against all grids using glide XP, keep max. 5 poses per ligand
- automated pose selection (using custom python script)
for each ligand merge poses from all grids and rank by XP glide docking score
pick pose with best XP glide docking score as best pose
select 4 additional pose by going down the ranked poses and picking new poses that are different enough from existing ones (using an RMSD cutoff of 1.0 A)
Ensemble docking protocol was tested first with set of PDB ligands. Good results for most ligands (both self- and cross-docking) although in some cases the docking score could not rank accurately the first pose.