Biomacromolecular structure visualization
and validation
Radka Svobodová
CEITEC, Masaryk University
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.
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
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.
ValTrendsDB
Protein quality and resolution :-)
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Cytochrome P450: Dependency of clashscore on year of release
ValTrendsDB
Example of analysis
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Cryo-EM
All structures
It looks, Cryo-EM structures have
much lower quality than common
structures
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