Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

Abstract

In protein-ligand binding, the electrostatic environments of the two binding partners may vary significantly in bound and unbound states, which may lead to protonation changes upon binding. In cases where ligand binding results in a net uptake or release of protons, the free energy of binding is pH-dependent. Nevertheless, conventional free energy… (More)
DOI: 10.1021/jp505777n

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