HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB. In CEITEC Joint Retreat 2019. 2019. ISBN 978-80-210-9300-3.
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Basic information
Original name Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB
Authors HORSKÝ, Vladimír (203 Czech Republic, guarantor, belonging to the institution), Veronika BENDOVÁ (203 Czech Republic, belonging to the institution), Dominik TOUŠEK (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
Edition CEITEC Joint Retreat 2019, 2019.
Other information
Original language English
Type of outcome Conference abstract
Field of Study 10608 Biochemistry and molecular biology
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
WWW Book of abstracts
RIV identification code RIV/00216224:14740/19:00110334
Organization unit Central European Institute of Technology
ISBN 978-80-210-9300-3
Keywords in English 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
Tags rivok
Tags International impact
Changed by Changed by: Mgr. Pavla Foltynová, Ph.D., učo 106624. Changed: 26/3/2020 16:52.
Abstract
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.
Links
LQ1601, research and development projectName: CEITEC 2020 (Acronym: CEITEC2020)
Investor: Ministry of Education, Youth and Sports of the CR
MUNI/A/1503/2018, interní kód MUName: Matematické statistické modelování 3 (Acronym: MaStaMo3)
Investor: Masaryk University, Category A
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