1. Flexible Receptor Side-Chain Docking

Standard docking assumes a rigid macromolecular backbone and sidechain geometry. However, catalytic residues frequently rotate to accommodate bulky or charged functional groups. AutoDock Vina supports explicit sidechain flexibility:

# Specify flexible catalytic residues (e.g., Chain A: His41, Cys145, Met165)
prepare_flexreceptor4.py -r target.pdbqt -s "A:41_A:145_A:165"

# Executes docking with both rigid and flexible receptor PDBQT inputs
vina --receptor target_rigid.pdbqt \
     --flex target_flex.pdbqt \
     --ligand drug.pdbqt \
     --config config.txt \
     --out docked_flex_out.pdbqt

2. Molecular Dynamics (MD) Ensemble Docking

When significant receptor backbone movements occur (e.g., kinase activation loop opening or GPCR extracellular loop breathing), flexible sidechain docking is insufficient. Ensemble docking addresses this limitation:

1. Run a 100–500 ns Molecular Dynamics (MD) simulation of the apo or holo target in explicit water using GROMACS or AMBER.
2. Extract structural trajectory frames (every 100 ps).
3. Perform RMSD-based conformational clustering (GROMACS gmx cluster using the GROMOS method with an active-site cutoff $\approx 1.2\text{ \AA}$).
4. Select the central representative frame from the top 5 most populated structural clusters.
5. Dock candidate ligand libraries across all 5 ensemble conformations and assign the hit score as the most favorable binding free energy across the ensemble.

3. Covalent Docking & Metal Coordination