SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Validation of ligands in macromolecular structures determined by X-ray crystallography. Acta Crystallographica Section D. 2018, vol. 74, No 3, p. 228-236. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318002541. |
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@article{1410438, author = {Smart, Oliver S. and Horský, Vladimír and Gore, Swanand and Svobodová Vařeková, Radka and Bendová, Veronika and Kleywegt, Gerard J. and Velankar, Sameer}, article_number = {3}, doi = {http://dx.doi.org/10.1107/S2059798318002541}, keywords = {PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB}, language = {eng}, issn = {2059-7983}, journal = {Acta Crystallographica Section D}, title = {Validation of ligands in macromolecular structures determined by X-ray crystallography}, url = {https://journals.iucr.org/d/issues/2018/03/00/ba5278/index.html}, volume = {74}, year = {2018} }
TY - JOUR ID - 1410438 AU - Smart, Oliver S. - Horský, Vladimír - Gore, Swanand - Svobodová Vařeková, Radka - Bendová, Veronika - Kleywegt, Gerard J. - Velankar, Sameer PY - 2018 TI - Validation of ligands in macromolecular structures determined by X-ray crystallography JF - Acta Crystallographica Section D VL - 74 IS - 3 SP - 228-236 EP - 228-236 SN - 20597983 KW - PDB KW - Protein Data Bank KW - three-dimensional macromolecular structure KW - validation KW - ligands KW - ValTrendsDB UR - https://journals.iucr.org/d/issues/2018/03/00/ba5278/index.html L2 - https://journals.iucr.org/d/issues/2018/03/00/ba5278/index.html N2 - 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. ER -
SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Validation of ligands in macromolecular structures determined by X-ray crystallography. \textit{Acta Crystallographica Section D}. 2018, vol.~74, No~3, p.~228-236. ISSN~2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318002541.
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