*MolProbity* is a web-based structure validation tool designed for proteins and nucleic acids, providing comprehensive and robust evaluation of model quality at both global and local levels. It leverages optimized hydrogen placement and all-atom contact analysis, complemented by updated covalent-geometry and torsion-angle criteria. The tool allows users to upload coordinate files, add and optimize hydrogen atoms, and perform various validation analyses, including all-atom contact analysis, torsion-angle combinations, covalent-geometry analyses, and nucleic acid-specific analyses. Results are presented in charts and graphical forms, aiding in manual rebuilding. *MolProbity* has significantly improved the quality of crystallographic models, as evidenced by its impact on the PDB database, where median values for various validation criteria have steadily improved since 2003. The tool is freely available for download and can be run as a local server, offering both web and command-line interfaces.*MolProbity* is a web-based structure validation tool designed for proteins and nucleic acids, providing comprehensive and robust evaluation of model quality at both global and local levels. It leverages optimized hydrogen placement and all-atom contact analysis, complemented by updated covalent-geometry and torsion-angle criteria. The tool allows users to upload coordinate files, add and optimize hydrogen atoms, and perform various validation analyses, including all-atom contact analysis, torsion-angle combinations, covalent-geometry analyses, and nucleic acid-specific analyses. Results are presented in charts and graphical forms, aiding in manual rebuilding. *MolProbity* has significantly improved the quality of crystallographic models, as evidenced by its impact on the PDB database, where median values for various validation criteria have steadily improved since 2003. The tool is freely available for download and can be run as a local server, offering both web and command-line interfaces.