Publication details

Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB

Authors

HORSKÝ Vladimír BENDOVÁ Veronika TOUŠEK Dominik SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav

Year of publication 2019
Type Conference abstract
MU Faculty or unit

Central European Institute of Technology

Citation
Description 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.
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