I wish to compute the binding energy of the ligand to the known cavity of the receptor.

My idea was to:

  1. Perform docking to the recognized binding site using AutoDock Vina
  2. Export bound ligands and interacting aminoacids using Chimera
  3. Run optimization on the ligand-aminoacids system (ONIOM; high layer ligand: B3LYP/6-31+G(d,p); low layer aminoacids: PM6), ligand alone (B3LYP/6-31+G(d,p), and aminoacids alone (PM6). These along with empirical dispersion GD3 and PCM water solvent.
  4. Recompute single point energies using larger basis set, like B3LYP/def2TZVP
  5. Compute the binding energy according to the equation: ΔE=[E(system)-E(ligand)+E(aminoacids)]
  6. Assess binding affinity (K) as: K=e^(-ΔE/RT)

Could someone confirm whether this is a valid pathway? If no, what shall be changed?



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.