Problems of robustness in Poisson-Boltzmann binding free energies

Although models based on the Poisson–Boltzmann (PB) equation have been fairly successful at predicting some experimental quantities, such as solvation free energies (ΔG), these models have not been consistently successful at predicting binding free energies (ΔΔG). Here we found that ranking a set of protein–protein complexes by the electrostatic component (ΔΔGel) of ΔΔG was more difficult than ranking the same molecules by the electrostatic component (ΔGel) of ΔG. This finding was unexpected because ΔΔGel can be calculated by combining estimates of ΔGel for the complex and its components with estimates of the ΔΔGel in vacuum. One might therefore expect that if a theory gave reliable estimates of ΔGel, then its estimates of ΔΔGel would be reliable. However, ΔΔGel for these complexes were orders of magnitude smaller than ΔGel, so although estimates of ΔGel obtained with different force fields and surface definitions were highly correlated, similar estimates of ΔΔGel were often not correlated.