Structure validation
Introduction


Low quality structures: We can not use them!
•Garbage in garbage out
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Garbage in, garbage out – how bad data can fuel bad decisions

Validation – beginning
•Great structural biology results, excellent papers
•2006: First problems - retraction of papers because wrong 3D structure data:
•Matthews B.W. (2007) Five retracted structure reports: inverted or incorrect? Protein science, 16,
1013–6.
•Johnston C.A., Kimple A.J., Giguere P.M., Siderovski D.P. (2008) RETRACTED: Structure of the
Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gb1g2. Structure, 16,
1086–1094.
•2008: X-ray Validation Task Force
•Read R.J. et. al (2011). A new generation of crystallographic validation tools for the protein
data bank. Structure, 19(10), 1395-1412.
•2009: NMR Validation Task Force
•Montelione G.T., et al. (2013). Recommendations of the wwPDB NMR validation task force. Structure,
21(9), 1563-1570.
•2010: Electron Microscopy Validation Task Force
•Henderson R., (2012). Outcome of the first electron microscopy validation task force meeting.
Structure, 20(2), 205-214.
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Nightmare before Christmas

•2015 ValidatorDB
•Sehnal D., Svobodová R., et al (2015). ValidatorDB: database of up-to-date validation results for
ligands and non-standard residues from the Protein Data Bank. Nucleic acids research, 43(D1),
D369-D375.
•2016 wwPDB/CCDC/D3R Ligand Validation Workshop
•Adams P.D. …, Svobodová R., … (2016). Outcome of the first wwPDB/CCDC/D3R ligand validation
workshop. Structure, 24(4), 502-508.
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Ligand Validation Workshop Group Photo 2015-07-30
Validation – ligands

Validation – reports and metrics
•2017 Validation reports
•Gore S., García E.S., Hendrickx P.M., Gutmanas A., Westbrook J.D., Yang H., ..., Kleywegt G.J.
(2017). Validation of structures in the Protein Data Bank. Structure, 25(12), 1916-1927.
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• 2018 Combined validation metrics
•Smart O.S., Horský V., Gore S., Svobodová R., Bendová V., Kleywegt G.J., Velankar S. (2018).
Worldwide Protein Data Bank validation information: usage and trends. Acta Crystallographica
Section D: Structural Biology, 74(3), 237-244.
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Vladimír Horský

Validation: Does it help?
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Obsah obrázku text, diagram, řada/pruh, Vykreslený graf Popis byl vytvořen automaticky
Horský V., Bendová V., Toušek D., Koča J.,  Svobodová R. (2019). ValTrendsDB: bringing Protein Data
Bank validation information closer to the user. Bioinformatics, 35(24), 5389-5390.
Obsah obrázku text, diagram, Paralelní, řada/pruh Popis byl vytvořen automaticky Obsah obrázku
text, diagram, řada/pruh, Paralelní Popis byl vytvořen automaticky

Validation – lectures today
•Protein validation
•Ligand validation
•Validation trends