The results of protein pKa calculations are routinely being analysed to understand the pH-dependence of protein characteristics such as stability and catalysis. Systems of functionally important titratable groups are identified from protein from pKa calculations, but the rationalisation of the behaviour of such systems is inherently problematic due to a lack of theoretical tools and methods. I present a number of novel methods for analysing the results of protein pKa calculations which have been embedded in a graphical user interface (pKaTool). In the present paper I present novel methods for assessing the reliability of protein pKa calculations and for analysing the roles of individual residues in determining active site pKa values and the pH-dependence of protein stability. The methods presented are freely available to academic researchers at http://enzyme.ucd.ie/Science/pKa/pKaTool .
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