Three methods, quantum mechanical and molecular mechanical polarizable continuum model (QM/MM/PCM), QM/PCM, and empirical, were developed and applied to calculate protein reduction potential (
E
0
) and p
K
a
values. In the QM/MM/PCM calculation of Lys55 p
K
a
of turkey ovomucoid third domain (OMTKY3), the MP2/6‐31 + G(2d,p) method was used to describe the QM region consisting of ∼45 atoms; the rest of the protein was modeled either with ab initio‐derived electric multipole points or atomic charges from standard force field methods; and the aqueous solvation effect was described with the polarizable continuum model (PCM). The calculated Lys55 p
K
a
values are in good agreement with experiments. QM/PCM methods were used to calculate p
K
a
values of various proteins and the
E
0
of type‐1 Cu centers. For solvent‐exposed p
K
a
sites, QM/PCM (MP2/6‐31 + G(2d,p) for ∼100 atoms, PCM with dielectric = 78.39 for aqueous solution) methods can often reproduce experimental p
K
a
values. For type‐1 Cu
E
0
, because of protein burial, the desolvation effect becomes significant: it was found that Cu‐ligand interactions and desolvation can potentially change the
E
0
by ∼300 and ∼400 mV, respectively, using the CPCM/B3LYP/6‐311++G(2df,p) method and model molecules of ∼100 atoms. An empirical method, PROPKA, was developed for protein p
K
a
calculation and analysis, which is able to calculate the p
K
a
values of a protein within ∼1 s.