Figure 1
From: Large-scale application of free energy perturbation calculations for antibody design
Schematics for the FEP calculations in this study. The free energy differences \({\Delta G}^{\mathrm{Complex}}\), \({\Delta G}^{\mathrm{Antibody}}\), and \({\Delta G}^{\mathrm{Peptide}}\) 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 (\({\Delta \Delta G}^{\mathrm{Binding}}\)) and the stability (\({\Delta \Delta G}^{\mathrm{Stability}}\)) of the antibody. The illustrated protein structures are from the m396 antibody25, rendered by the VMD program43 (version 1.9.3).
