H++ is a web server that estimates pKa values and adds missing hydrogens to macromolecules. It automates the process of predicting protonation states and titration curves based on atomic-resolution structures. The server allows both experts and novices to quickly obtain estimates of pKa values, isoelectric points, and other related characteristics of biomolecules. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH. The output is in the PQR format and includes coordinate and topology files in the format supported by the molecular modeling package AMBER. 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 server uses the standard continuum solvent methodology, either the generalized Born (GB) or the Poisson-Boltzmann (PB) model, as requested by the user. All steps of the computational process are fully automated. Commonly used input parameters are accessible via a simple interface that provides reasonable defaults. The server is designed to automate the prediction of pKa and protonation states of ionizable residues in macromolecules using atomic resolution structures as input. The output structure contains missing hydrogens added according to calculated protonation states and is available in several formats used by a number of popular molecular modeling packages. The calculations are based on the standard continuum solvent methodology, which has been successfully used for this purpose over more than a decade. The server is expected to become a useful tool for the broad biochemical, structural, and computational biology community, as well as drug designers. It can also be a useful educational resource.H++ is a web server that estimates pKa values and adds missing hydrogens to macromolecules. It automates the process of predicting protonation states and titration curves based on atomic-resolution structures. The server allows both experts and novices to quickly obtain estimates of pKa values, isoelectric points, and other related characteristics of biomolecules. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH. The output is in the PQR format and includes coordinate and topology files in the format supported by the molecular modeling package AMBER. 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 server uses the standard continuum solvent methodology, either the generalized Born (GB) or the Poisson-Boltzmann (PB) model, as requested by the user. All steps of the computational process are fully automated. Commonly used input parameters are accessible via a simple interface that provides reasonable defaults. The server is designed to automate the prediction of pKa and protonation states of ionizable residues in macromolecules using atomic resolution structures as input. The output structure contains missing hydrogens added according to calculated protonation states and is available in several formats used by a number of popular molecular modeling packages. The calculations are based on the standard continuum solvent methodology, which has been successfully used for this purpose over more than a decade. The server is expected to become a useful tool for the broad biochemical, structural, and computational biology community, as well as drug designers. It can also be a useful educational resource.