The MM-SCP has been applied to predict pKa values of titratable residues in wild type and mutants of staphylococcal nuclease (SNase). The calculations were based on crystal structures made available by the Garcia-Moreno Laboratory. In the mutants, mostly deeply buried hydrophobic residues were replaced with ionizable residues, and thus their pKa values could be measured and calculated using various methods. The data set used here consisted of a set of WT SNase for which His pKa at several ionic strengths had been measured, a set of mutants for which measured pKa were available and a set of 11 mutants for which the measured pKa were not known at the time of calculation. For this latter set, blind predictions were submitted to the protein pKa cooperative, 2009 workshop at Telluride, where the results of the blind predictions were discussed (the RMSD of the submitted set was 1.10 pH units). The calculations on the structures with known pKa indicated that in addition to weaknesses of the method, structural issues were observed that led to larger errors (>1) in pKa predictions. For example, different crystallographic conditions or steric clashes can lead to differences in the local environment around the titratable residue, which can produce large differences in the calculated pKa. To gain further insight into the reliability of the MM-SCP, pKa of an extended set of 54 proteins belonging to several structural classes were carried out. Here some initial results from this study are reported to help place the SNase results in the appropriate context. Proteins 2011. © 2011 Wiley-Liss, Inc.