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@proceedings{1548689,
author = {Horský, Vladimír and Bendová, Veronika and Toušek, Dominik and Svobodová Vařeková, Radka and Koča, Jaroslav},
booktitle = {CEITEC Joint Retreat 2019},
keywords = {PDB; PDBe; Protein Data Bank; three-dimensional macromolecular structure; validation; wwPDB validation pipeline; ligands; ValTrendsDB; X-ray crystallography; NMR spectroscopy; 3DEM; database; trends in quality; visualization; statistical analysis},
language = {eng},
isbn = {978-80-210-9300-3},
title = {Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB},
url = {http://phdretreat.ceitec.cz/download/220},
year = {2019}
}
TY - CONF
ID - 1548689
AU - Horský, Vladimír - Bendová, Veronika - Toušek, Dominik - Svobodová Vařeková, Radka - Koča, Jaroslav
PY - 2019
TI - Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB
SN - 9788021093003
KW - PDB
KW - PDBe
KW - Protein Data Bank
KW - three-dimensional macromolecular structure
KW - validation
KW - wwPDB validation pipeline
KW - ligands
KW - ValTrendsDB
KW - X-ray crystallography
KW - NMR spectroscopy
KW - 3DEM
KW - database
KW - trends in quality
KW - visualization
KW - statistical analysis
UR - http://phdretreat.ceitec.cz/download/220
L2 - http://phdretreat.ceitec.cz/download/220
N2 - Improvements of methods for biomacromolecular structure acquisition have in recent decades come hand in hand with the rising importance of biomacromolecular structural data. However, the experimental nature of such methods has led to the occurrence of errors in structure models, which in turn were responsible for retraction of several articles from esteemed journals. Scientific community reacted to the emergence of this phenomenon by developing, utilizing, and propagating various software tools that validated geometric quality and adherence of structure model to the underlying experimental data. The Protein Data Bank (PDB), the largest database of structures of biomacromolecular complexes, deployed their own validation pipeline that checks nearly every structure stored in the database. With the emergence of tangible focus on quality, we were curious whether it had any impact on newer structures. To provide food for thought for these questions, we have carried out a wide range exploratory analysis of trends between quality and features of structures of biomacromolecular complexes. Results of this analysis are presented using interactive information-rich plots in the ValTrendsDB database (ncbr.muni.cz/ValTrendsDB). Recently, we have added new functionality to the weekly-updated ValTrendsDB database that enables users to interactively explore trends from the analysis and compare them to user-defined sets of structures, e.g., structures of a journal, protein family, experimental method, or structures from an author.
ER -
HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB. In \textit{CEITEC Joint Retreat 2019}. 2019. ISBN~978-80-210-9300-3.
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