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@proceedings{1415496,
author = {Smart, Oliver S. and Horský, Vladimír and Gore, Swanand and Svobodová Vařeková, Radka and Bendová, Veronika and Kleywegt, Gerard J. and Velankar, Sameer},
booktitle = {CEITEC PhD and Postdoc Retreat 2018},
keywords = {PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB},
language = {eng},
isbn = {978-80-210-8941-9},
title = {Bringing validation information closer to the user},
year = {2018}
}
TY - CONF
ID - 1415496
AU - Smart, Oliver S. - Horský, Vladimír - Gore, Swanand - Svobodová Vařeková, Radka - Bendová, Veronika - Kleywegt, Gerard J. - Velankar, Sameer
PY - 2018
TI - Bringing validation information closer to the user
SN - 9788021089419
KW - PDB
KW - Protein Data Bank
KW - three-dimensional macromolecular structure
KW - validation
KW - ligands
KW - ValTrendsDB
N2 - Universal availability of biomacromolecular structural data has gradually changed life sciences. Various databases, the most prominent being the Protein Data Bank (PDB), enable access to plethora of published structures. Unfortunately, questions regarding quality of structure models have increased in importance in recent years. Therefore, all new structures are validated at the time of their submission to PDB. Here, we show how values of available validation metrics can be combined into an overall score that enables ranking of macromolecular structures and their domains in search results. This solution brings validation information closer to the general scientific community. A big challenge of crystallographic studies is how to correctly interpret electron density that is present in the binding site. It either represents an expected ligand, or just solvent molecules. As a result, ligand model quality in the PDB database was and still remains a concerning matter. That is why several ligand validation methods have been integrated into the PDB validation pipeline. Here, we describe these methods, along with our finding that the currently used LLDF metric can give misleading results.
ER -
SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT a Sameer VELANKAR. Bringing validation information closer to the user. In \textit{CEITEC PhD and Postdoc Retreat 2018}. 2018. ISBN~978-80-210-8941-9.
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