Author response image 4. The explicit-ion model predicts the binding affinities of protein-DNA complexes well, related to Fig.

1 of the main text. Experimental and simulated binding free energies are compared for nine protein-DNA complexes [cite], with a Pearson Correlation coefficient of 0.6. The PDB ID for each complex is indicated in red, and the diagonal line is drawn in blue. The significant correlation between simulated and experimental values supports the accuracy of the model. To further enhance the agreement between the two, it will be necessary to implement specific non-bonded interactions that can resolve differences among amino acids and nucleotides beyond simple electrostatics. Such modifications will be interesting avenues for future research. See text Section: Binding free energy of protein-DNA complexes for simulation details.