TABLE 9.

Summary of pK_a shifts, calculated with PB/LRA, the “standard” PB protocol and MDFE

			Standard‡
Residue	Pathway*	PB/LRA†	Cavity	No cavity§	MDFE	Experiment
Thioredoxin Asp-26	3-point	5.8(1.5)	1.4/−0.7¶	0.0/−1.4	7.8	3.5
RNase Asp-14	3-point	−1.4(1.5)	2.2/0.0	−0.7/−2.0	0.0	<−2.0
Thioredoxin Asp-20	3-point	3.7(0.4)	2.2/1.4	0.8/0.7	0.6	0.0

^*The pathways have been explained in Table 2 and refer to the PB/LRA entries.

^†The PB/LRA values correspond to averages of the results with and

^‡Using a protein dielectric of 20.

^§The side chain is embedded directly in the protein medium (see “Comparison to a standard pK_a protocol”).

^¶Throughout the table, x/y denote results using structures from the protonated/ionized state.