The pK(a) values in proteins govern the pH-dependence of protein stability and enzymatic activity. A large number of mutagenesis experiments have been carried out in the last three decades to re-engineer the pH-activity and pH-stability profile of enzymes and proteins. We have developed the pKD webserver (http://polymerase.ucd.ie/pKa_Design), which predicts sets of point mutations that will change the pK(a) values of a set of target residues in a given direction, thus allowing for targeted re-design of the pH-dependent characteristics of proteins. The server provides the user with an interactive experience for re-designing pK(a) values by pre-calculating DeltapK(a) values from all feasible point mutations. Design solutions are found in less than 10 min for a typical design job for a medium-sized protein. Mutant DeltapK(a) values calculated by the pKD web server are in close agreement with those produced by comparing results from full-fledged pK(a) calculation methods.
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