Evaluating the Reliability of MM-PB/GB-SA Method for the Protein-Ligand Binding Free Energies Using Penicillopepsin-Inhibitor ligands

An accurate prediction of the ligand-receptor binding free energies (ΔG) is a critical step in early stages rational drug design. The Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method popular
 
 approach to estimate ΔG. However, correlations between predicted and experimental ΔG are variable. goal this study investigate various approaches optimize accuracy MM-GBSA method. A molecular dynamic (MD) simulations protocol was applied using penicillopepsin receptor against its inhibitor ligands, repeated 50 times for each complex system. After that, five inhibitors were Moreover, diverse values calculated from replicate MD results showed not only affinities systems but also root-mean-square deviation. In addition, statistical analysis evaluated sample size.