QVADIS: A package to compute proton transfer pathways in proteins

Abstract

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 re- trace 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.