2.5 Binding free energy
Eventually, a thorough analysis of the binding free energy
(∆Gbind) of all selected scaffolds was carried out using
Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) protocol
by the g-mmpbsa package [15]. MM-PBSA analysis gives a detailed
estimation of the binding affinity of protein-ligand interaction. To
calculate the total ∆Gbind, the free polar solvation
energy, SASA energy, and potential energy (Van der Waals and
electrostatic interactions) of each protein-ligand complex were
analyzed.