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

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Authors	SMART Oliver S. HORSKÝ Vladimír GORE Swanand SVOBODOVÁ VAŘEKOVÁ Radka BENDOVÁ Veronika KLEYWEGT Gerard J. VELANKAR Sameer
Year of publication	2018
Type	Article in Periodical
Magazine / Source	Acta Crystallographica Section D
MU Faculty or unit	Central European Institute of Technology
Citation
Web	https://journals.iucr.org/d/issues/2018/03/00/ba5278/index.html
Doi	http://dx.doi.org/10.1107/S2059798318002541
Keywords	PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB
Description	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.
Related projects:	ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences Czech National Infrastructure for Biological Data CEITEC 2020 Matematické statistické modelování 2