Probing the mechanism of peptide binding to REV response element RNA of HIV-1; MD simulations and free energy calculations

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

“…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. They have proven to be reliable methods for the computation of binding energy leading to numerous applications in small-molecule ligand binding and drug design [20] , [21] , [22] , protein-peptide interactions [23] , [24] , [25] , [26] , protein-protein interactions [27] , [28] and protein design [29] , [30] . Although their accuracy in some systems is in the order of 10 kJ/mol, both computational improvements in the calculation of individual terms of the binding energy as well as carrying out many short MD simulations [31] , [32] has helped obtain more accurate estimations of binding energies up to the 1 kJ/mol range.…”