Propka is a tool to modify the protonation state of a protein structure in the protein data bank (pdb) format to match a given pka value. it can also be used to refine nmr structures, which often yield inaccurate pka values for some residues.

the propka method is described in hui li, andrew d. robertson, and jan h. jensen "very fast empirical prediction and interpretation of protein pka values" proteins, 2005, 61, 704-721