H++ is a web server that automates the estimation of pKa values and the addition of missing hydrogens to macromolecules based on their atomic-resolution PDB structures. It provides a tool for both experts and novices to quickly obtain estimates of pKa values, isoelectric points, titration curves, and protonation microstate energies. The server adds protons to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH, and outputs the structure in PQR format. It also generates coordinate and topology files in the format supported by the AMBER molecular modeling package. The calculations are based on the continuum electrostatics methodology, using either the generalized Born (GB) or Poisson–Boltzmann (PB) models. The server automates the entire process, including pre-processing of input structures, addition of missing atoms, and electrostatic calculations. It also generates titration curves, pK1/2 values, and protonation states for each titratable group. The server is intended for a broad community of biochemists, molecular modelers, structural biologists, and drug designers, and can also be used as an educational tool in biochemistry courses. The calculations are based on the established continuum electrostatics methodology, which has been successfully used for this purpose over more than a decade. H++ is expected to become a useful tool for the biochemical, structural, and computational biology community, as well as for drug designers.H++ is a web server that automates the estimation of pKa values and the addition of missing hydrogens to macromolecules based on their atomic-resolution PDB structures. It provides a tool for both experts and novices to quickly obtain estimates of pKa values, isoelectric points, titration curves, and protonation microstate energies. The server adds protons to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH, and outputs the structure in PQR format. It also generates coordinate and topology files in the format supported by the AMBER molecular modeling package. The calculations are based on the continuum electrostatics methodology, using either the generalized Born (GB) or Poisson–Boltzmann (PB) models. The server automates the entire process, including pre-processing of input structures, addition of missing atoms, and electrostatic calculations. It also generates titration curves, pK1/2 values, and protonation states for each titratable group. The server is intended for a broad community of biochemists, molecular modelers, structural biologists, and drug designers, and can also be used as an educational tool in biochemistry courses. The calculations are based on the established continuum electrostatics methodology, which has been successfully used for this purpose over more than a decade. H++ is expected to become a useful tool for the biochemical, structural, and computational biology community, as well as for drug designers.