Let us show first that a calculation with flexible protein gives a reasonable prediction of the binding free energy. To do that we selected a set of ~200 protein - ligand complexes from the BindingDB database. The protein-ligand pairs were selected mainly so that the complex is small and therefore the whole calculation is fast. The results are represented on the Figure. The horizontal and the vertical axis represent the calculated and the experimental value of the binding free energy calculated from the complexed positions of the ligand within the protein.
The correlation is clearly there and in a few days I will show that the calculated values demonstrate not only the accuracy, but also a good selectivity.
The other Figure represents the correlation be
