Validation of ligands in macromolecular structures determined by X-ray crystallography

• Autoři: SMART Oliver S.; HORSKÝ Vladimír; GORE Swanand; SVOBODOVÁ VAŘEKOVÁ Radka; BENDOVÁ Veronika; KLEYWEGT Gerard J.; VELANKAR Sameer
• Rok publikování: 2018
• Druh: Článek v odborném periodiku
• Časopis / Zdroj: Acta Crystallographica Section D
• Fakulta / Pracoviště MU: Středoevropský technologický institut
• www: https://journals.iucr.org/d/issues/2018/03/00/ba5278/index.html
• Doi: http://dx.doi.org/10.1107/S2059798318002541
• Klíčová slova: PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB
• Popis: The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. In this article, the ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

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