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- Introduction to model quality assessment
- Local quality assessment
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Tools for stereochemical validation
Tools like MolProbity (Chen et al., 2010) are widely used to calculate and assess many of these chemical and physical quality metrics based on prior knowledge. MolProbity performs detailed checks at the local level (per-residue, per-atom, per-bond) and then calculates the global summary statistics (like Ramachandran outlier percentage, sidechain outlier percentage, bond/angle deviations, and clashscore).
Additional resources
| Tool | Description |
| CheckMyMetal | Quality scores of a protein are displayed in the context of all known protein structures, and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. |
| MolProbity | It calculates the Ramachandran-Z score and the rotamer Z-score. |
| Prosa-web | Quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. |
| Tortoize | Focuses on automating the final steps of the crystallographic process, i.e. the optimisation of the structure model through refinement and rebuilding. The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. |
| DNATCO | Web server that validates and analyses nucleic acid structures |
| Privateer | Web server for carbohydrate structure validation, refinement and analysis |
| PDB-REDO | A service that checks the metal binding site and validation |