Moreover, the RMSD value of the BACE_18 ligand was 2.08 Å and increased to 2.34 Å after MD. The analysis of the corresponding MD trajectory shows that the established interactions between the ligand and the aspartyl dyad are different from those before MD (Fig. ). This may be due to a wrong protonation of the aspartyl dyad residues at pH 4.5. The activity of BACE-1 is known to be pH-dependent, with a reported activity peak between pH 3.5 and 5.5 , which is why we protonated our proteins as appropriate for pH 4.5.