Proton transfer reactions play an important role in many areas of biology. We reimplemented a method introduced by Taraphder et al. to characterize putative proton transfer pathways in proteins along hydrogen bonded networks and could retrace their results on cytochrome P450cam. By combining this method with our established Q-HOP approach to compute proton transfer probabilities we present here to our best knowledge for the first time a general program package to characterize proton transfer pathways in biomolecules accounting for both side chain flexibility and transfer kinetics.