Theoretical methods are a compelling alternative to experiments. Many of these are motivated ΔG s (A H , A -) ΔG s,p (A H ) ΔG s,p (A -) ΔG p (A H , A -) Figure : Thermodynamic cycle to compute the free energy difference between protonating a residue in a blocked peptide in solution and the same residue in a protein. This ∆∆G can be related to the pK a (protein) given the reference pK • a via Equation . by a free energy formalism based on the thermodynamic cycle shown in Figure . Here, we consider a residue of interest (A) in both the protein A p (Figure , right) and the reference peptide in solution A s (Figure , left). We assume that the reference pK • a is known; then pK a (protein) is given by pK a (protein