Figure 1.

Schematics for the FEP calculations in this study. The free energy differences ${\mathrm{\Delta }G}^{\mathrm{Complex}}$, ${\mathrm{\Delta }G}^{\mathrm{Antibody}}$, and ${\mathrm{\Delta }G}^{\mathrm{Peptide}}$ between systems with residues $a$ and $b$ are obtained from the corresponding FEP simulations, and the results further determine (Eqs. (1) and (2)) the effect of mutation on the binding (${\mathrm{\Delta }\mathrm{\Delta }G}^{\mathrm{Binding}}$) and the stability (${\mathrm{\Delta }\mathrm{\Delta }G}^{\mathrm{Stability}}$) of the antibody. The illustrated protein structures are from the m396 antibody²⁵, rendered by the VMD program⁴³ (version 1.9.3).