3.5.4. MM-GBSA Energy Calculations

Molecular docking is a robust technique for determining the binding orientation of a protein–ligand complex. However, it is still lacking in its ability to correctly identify the binding affinities of docked ligands. In order to determine correct binding energies of docked conformations, MM-GBSA energy calculations were performed, which are an efficient and reliable method for the determination of binding free energies. The MM-GBSA method provides free energy calculations by taking into account all hydrophobic, hydrophilic and electrostatic interactions [63]. After energy calculations, values obtained were more negative and showed stronger binding affinities, as compared to the docking scores obtained from molecular docking. The following equation was used to calculate binding free energy [64];

$$
\Delta \mathbf{G}\_{\text{bind}} = \Delta \mathbf{E}\_{\text{mm}} + \Delta \mathbf{G}\_{\text{sol}} + \Delta \mathbf{G}\_{\text{SA}}
$$

The MM-GBSA energies for the protein–ligand complex was determined through the Thermal\_mmgbsa script of Schrodinger. MM-GBSA energies are tabulated in Table 7.


**Table 7.** MM-GBSA binding energies of Dabrafenib docked at active site of NEK7.

3.5.5. MM-PBSA Energy Calculations

In MMPBSA energy analysis, the free binding energies of protein, ligand and protein– ligand complex are estimated by following equation;

$$\rm{G} = \rm{E\_{bnd}} + \rm{E\_{el}} + \rm{E\_{vdW}} + \rm{G\_{pol}} + \rm{G\_{np}} - \rm{TS}$$

where, Ebnd I refers to bond energy, Eel refers to electrostatic energy and EvdW represents van der Waals interactions. In the current study, Poisson–Boltzmann calculations were performed using the internal PBSA solver in mmpbsa\_py\_energy. All units are represented in kcal/mol. MM-PBSA energy analysis is given in Table 8.


**Table 8.** MM-PBSA binding energies of Dabrafenib docked at active site of NEK7.
