MolProbity is a web-based tool for validating 3D structures of proteins, nucleic acids, and complexes. It offers detailed all-atom contact analysis, updated dihedral-angle diagnostics, and the ability to calculate and display hydrogen bond and van der Waals contacts. The tool adds and optimizes hydrogen atoms, corrects flipped Asn, Gln, and His sidechains, and uses high-accuracy Ramachandran and rotamer distributions to identify conformational outliers. MolProbity provides multiple output formats, including downloadable PDB files, graphics, and 3D kinemage graphics for online viewing. It supports both X-ray and NMR structures and is useful for both structure consumers and producers. The tool has been continuously operational for over 5 years, with significant improvements in recent years, including faster hydrogen optimization and enhanced user interface. MolProbity is freely available at http://molprobity.biochem.duke.edu.MolProbity is a web-based tool for validating 3D structures of proteins, nucleic acids, and complexes. It offers detailed all-atom contact analysis, updated dihedral-angle diagnostics, and the ability to calculate and display hydrogen bond and van der Waals contacts. The tool adds and optimizes hydrogen atoms, corrects flipped Asn, Gln, and His sidechains, and uses high-accuracy Ramachandran and rotamer distributions to identify conformational outliers. MolProbity provides multiple output formats, including downloadable PDB files, graphics, and 3D kinemage graphics for online viewing. It supports both X-ray and NMR structures and is useful for both structure consumers and producers. The tool has been continuously operational for over 5 years, with significant improvements in recent years, including faster hydrogen optimization and enhanced user interface. MolProbity is freely available at http://molprobity.biochem.duke.edu.