SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Bringing validation information closer to the user. In CEITEC PhD and Postdoc Retreat 2018. 2018. ISBN 978-80-210-8941-9.
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Basic information
Original name Bringing validation information closer to the user
Authors SMART, Oliver S. (826 United Kingdom of Great Britain and Northern Ireland), Vladimír HORSKÝ (203 Czech Republic, guarantor, belonging to the institution), Swanand GORE (826 United Kingdom of Great Britain and Northern Ireland), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Veronika BENDOVÁ (203 Czech Republic, belonging to the institution), Gerard J. KLEYWEGT (528 Netherlands) and Sameer VELANKAR (826 United Kingdom of Great Britain and Northern Ireland).
Edition CEITEC PhD and Postdoc Retreat 2018, 2018.
Other information
Original language English
Type of outcome Presentations at conferences
Field of Study 10608 Biochemistry and molecular biology
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
RIV identification code RIV/00216224:14740/18:00102640
Organization unit Central European Institute of Technology
ISBN 978-80-210-8941-9
Keywords in English PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB
Tags rivok
Tags International impact
Changed by Changed by: Mgr. Vladimír Horský, Ph.D., učo 358970. Changed: 29/4/2018 17:17.
Abstract
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.
Links
MUNI/A/1204/2017, interní kód MUName: Matematické statistické modelování 2 (Acronym: MaStaMo2)
Investor: Masaryk University, Category A
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