The EM-based approach corresponds to PropKa calculations, while the ML-based pKa-ANI method is discussed in a separate section. With respect to the MDapproach, we observed two important sources of prediction inaccuracy: residue coupling and lysine parameterization. Adjusting the pK a calculation framework to account for these led to an adjusted estimate that we compare with the unadjusted one. This is extensively discussed in Determinants of accuracy.