What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?

A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity

“…The MM/PBSA and its variant MM/GBSA (Molecular Mechanics Poisson-Boltzmann Surface Area and Molecular Mechanics Generalized Born Surface Area) are popular methods used to determine the free binding energy between a protein and a ligand [16] , [17] , [18] , [19] . Essentially, these methods evaluate the free binding energy of the ligand from MD simulation snapshots using energy terms of the MD force field, but approximating the polar energy terms with the Poisson-Boltzmann (PB) equation, estimating the non-polar energy terms using the solvent-accessible surface area (SASA) method and roughly approximating the entropic terms using normal-mode analysis.…”

Designing of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches

“…This analysis was conducted to estimate binding free energies of the docked complexes to confirm the binding efficacy of the designed vaccine to immune cell receptors. The different free binding energies of the vaccine-MHC-I molecule, vaccine-MHC-II, and vaccine-TLR-4 molecule, as calculated in MM-GBSA and MM-PBSA [ 60 ] methods, are tabulated in Table 4 , respectively. The net value predicted in MM-GBSA was −456.67 kcal/mol, −387.17 kcal/mol, and −515.99 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively.…”

Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective

“…E gas is composed of electrostatic and van der Waals terms; Eele, EvdW, respectively. The polar solvation energy (E GB ) and nonpolar solvation energy (E SA ) are used to calculate the E sol [ 60 , 61 ].…”