ValTrendsDB: Viewing structure quality from macro and micro
perspective

a 2018

ValTrendsDB: Viewing structure quality from macro and micro perspective

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA

Základní údaje

Originální název

ValTrendsDB: Viewing structure quality from macro and micro perspective

Autoři

HORSKÝ, Vladimír (203 Česká republika, garant, domácí), Veronika BENDOVÁ (203 Česká republika, domácí), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, domácí)

Vydání

ELIXIR CZ Annual Conference 2018, 2018

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14310/18:00104935

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

PDB; Protein Data Bank; Chemical Component Dictionary; three-dimensional macromolecular structure; validation; validation metrics; density fit; visualization; ligands; ValTrendsDB; analysis of trends

Změněno: 16. 12. 2018 15:56, Mgr. Vladimír Horský, Ph.D.

Anotace

V originále

The general availability of data about biomacromolecular structures is a key success of life sciences. However, quality issues of structures have come into consideration when erroneous data caused retraction of articles from several journals. In reaction, scientific community began developing tools for validating biomacromolecular complexes. The PDB developed a validation pipeline, which provides users with a validation report. With this new source of quality data being available, we became curious whether they have any impact on quality of newly published biomacromolecules. Another concern of ours was whether ligands are sufficiently validated as well. To help answer these questions, we have performed analysis of trends in relationships of quality and features of biomacromolecules and their ligands. 88 factors have been considered in total. Metadata and quality data of structures came from the PDB. ValidatorDB database provided some of the ligand quality data. Some trends we discovered were expected (e.g., newer structures have better quality), while the existence of others was a surprise (e.g., ligand quality is stagnant at best, currently utilized structure validation methods do not validate ligands well). Discovered trends are presented in the ValTrendsDB database, where users can view all plots of relationships from the analysis. Additionally, it is possible to draw plots of any factor pair with custom settings, as well as view the value distribution of every factor. Recent update of the ValTrendsDB database implemented the functionality of visualizing values of one or more PDB entries in any plot. Entries to visualize in plots are provided via an embedded smart search field connected to the PDB database. Users can therefore view the quality of their structures of interest, e.g., structures of a journal, protein family, experimental method, or a specific author, in relation to the trend across the whole PDB database.

Návaznosti

MUNI/A/1204/2017, interní kód MU

Název: Matematické statistické modelování 2 (Akronym: MaStaMo2)

Investor: Masarykova univerzita, Matematické statistické modelování 2, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. ValTrendsDB: Viewing structure quality from macro and micro perspective. In ELIXIR CZ Annual Conference 2018. 2018.

@proceedings{1478656,
   author = {Horský, Vladimír and Bendová, Veronika and Svobodová Vařeková, Radka and Koča, Jaroslav},
   booktitle = {ELIXIR CZ Annual Conference 2018},
   keywords = {PDB; Protein Data Bank; Chemical Component Dictionary; three-dimensional macromolecular structure; validation; validation metrics; density fit; visualization; ligands; ValTrendsDB; analysis of trends},
   language = {eng},
   title = {ValTrendsDB: Viewing structure quality from macro and micro perspective},
   year = {2018}
}

TY  - CONF
ID  - 1478656
AU  - Horský, Vladimír - Bendová, Veronika - Svobodová Vařeková, Radka - Koča, Jaroslav
PY  - 2018
TI  - ValTrendsDB: Viewing structure quality from macro and micro perspective
KW  - PDB
KW  - Protein Data Bank
KW  - Chemical Component Dictionary
KW  - three-dimensional macromolecular structure
KW  - validation
KW  - validation metrics
KW  - density fit
KW  - visualization
KW  - ligands
KW  - ValTrendsDB
KW  - analysis of trends
N2  - The general availability of data about biomacromolecular structures is a key success of life sciences. However, quality issues of structures have come into consideration when erroneous data caused retraction of articles from several journals. In reaction, scientific community began developing tools for validating biomacromolecular complexes. The PDB developed a validation pipeline, which provides users with a validation report. With this new source of quality data being available, we became curious whether they have any impact on quality of newly published biomacromolecules. Another concern of ours was whether ligands are sufficiently validated as well. To help answer these questions, we have performed analysis of trends in relationships of quality and features of biomacromolecules and their ligands. 88 factors have been considered in total. Metadata and quality data of structures came from the PDB. ValidatorDB database provided some of the ligand quality data. Some trends we discovered were expected (e.g., newer structures have better quality), while the existence of others was a surprise (e.g., ligand quality is stagnant at best, currently utilized structure validation methods do not validate ligands well). Discovered trends are presented in the ValTrendsDB database, where users can view all plots of relationships from the analysis. Additionally, it is possible to draw plots of any factor pair with custom settings, as well as view the value distribution of every factor. Recent update of the ValTrendsDB database implemented the functionality of visualizing values of one or more PDB entries in any plot. Entries to visualize in plots are provided via an embedded smart search field connected to the PDB database. Users can therefore view the quality of their structures of interest, e.g., structures of a journal, protein family, experimental method, or a specific author, in relation to the trend across the whole PDB database.
ER  -

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. ValTrendsDB: Viewing structure quality from macro and micro perspective. In \textit{ELIXIR CZ Annual Conference 2018}. 2018.

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