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Validation - trends
Radka Svobodová
CEITEC, Masaryk University

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ValTrendsDB
§Database of biomacromolecular structure validation trends
§Based on structures from Protein Data Bank, automatic update
§http://ncbr.muni.cz/ValTrendsDB
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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.

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ValTrendsDB
§Validation of cytochromes P450 – overview of the whole family
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Blue points are structures of cytochromes P450-cam
Red points show a common trend

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Other projects: ValTrendsDB
§Database of biomacromolecular structure validation trends
§Based on structures from Protein Data Bank, automatic update
§http://ncbr.muni.cz/ValTrendsDB
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Author or co-author: R. Abagyan
All structures
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.

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ValTrendsDB
Protein quality and resolution :-)
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Cytochrome P450: Dependency of clashscore on year of release

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ValTrendsDB
Example of analysis
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Cryo-EM
All structures
It looks, Cryo-EM structures have much lower quality than common structures

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ValTrendsDB
Example of analysis
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Cryo-EM
All structures
Cryo-EM
All structures
It looks, Cryo-EM structures have much lower quality than common structures
But when we take into account a resolution, Cryo-EM structures have (for resolution > 2.4 Å) higher
quality