Exploring trends in quality and features of biomacromolecular
complexes with ValTrendsDB

a 2019

Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA, Radka SVOBODOVÁ VAŘEKOVÁ et. al.

Basic information

Original name

Exploring trends in quality and features of biomacromolecular complexes 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), Jaroslav KOČA (203 Czech Republic, belonging to the institution) and Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution)

Edition

XX. setkání biochemiků a molekulárních biologů, 2019

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Conference website

RIV identification code

RIV/00216224:14740/19:00111378

Organization unit

Central European Institute of Technology

ISBN

978-80-210-9420-8

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

Abstract

V originále

One of the most applauded achievements of life sciences is the availability of structural data of biomacromolecular complexes to the scientific public. Unfortunately, the concept of errors in structure models is not just theoretical. The community of structural biologists reacted to this phenomenon by developing and utilizing methodologies and software tools for structure model validation. The emergent focus on validation provoked us to ask: Does it have any impact on quality of new publicly available structures? We have carried out a wide range exploratory analysis of trends in relationships of pairs of factors that represent quality and features of biomacromolecules and ligands. We had two data sources for this analysis: Most data were obtained from the PDB database, while additional information concerning ligand quality was sourced from the ValidatorDB database. Some of the trends that we discovered were expected (e.g., newer structure models have, in general, higher quality than the older ones have), while other discovered trends were a surprise to us (e.g., ligand model quality is stagnant at best). The whole set of results of the exploratory analysis is available in our weekly-updated ValTrendsDB database. Users can view there all factor pair relationship plots of all trends discovered during the analysis. It is also possible to draw custom plots of any pair of factors with custom settings. Additionally, users are able to view value distribution of every factor considered. An important functionality of ValTrendsDB is the support for visualization of data points of a set of interesting PDB entries into any factor pair plot available, regardless of whether such plot is precomputed, or custom. With this functionality, users can view quality and features of their structure models of interest, e.g., structures of a journal, structures of a protein family, structures acquired using a particular experimental method, or structures assembled by specific authors, in relation to the trend across entries of the whole PDB database

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/1503/2018, interní kód MU

Name: Matematické statistické modelování 3 (Acronym: MaStaMo3)

Investor: Masaryk University, Category A

Citovat

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB. In XX. setkání biochemiků a molekulárních biologů. 2019. ISBN 978-80-210-9420-8.

@proceedings{1581336,
   author = {Horský, Vladimír and Bendová, Veronika and Toušek, Dominik and Koča, Jaroslav and Svobodová Vařeková, Radka},
   booktitle = {XX. setkání biochemiků a molekulárních biologů},
   keywords = {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},
   language = {eng},
   isbn = {978-80-210-9420-8},
   title = {Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB},
   url = {https://setkanibmb.webnode.cz/},
   year = {2019}
}

TY  - CONF
ID  - 1581336
AU  - Horský, Vladimír - Bendová, Veronika - Toušek, Dominik - Koča, Jaroslav - Svobodová Vařeková, Radka
PY  - 2019
TI  - Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB
SN  - 9788021094208
KW  - PDB
KW  - PDBe
KW  - Protein Data Bank
KW  - three-dimensional macromolecular structure
KW  - validation
KW  - wwPDB validation pipeline
KW  - ligands
KW  - ValTrendsDB
KW  - X-ray crystallography
KW  - NMR spectroscopy
KW  - 3DEM
KW  - database
KW  - trends in quality
KW  - visualization
KW  - statistical analysis
UR  - https://setkanibmb.webnode.cz/
L2  - https://setkanibmb.webnode.cz/
N2  - One of the most applauded achievements of life sciences is the availability of structural data of biomacromolecular complexes to the scientific public. Unfortunately, the concept of errors in structure models is not just theoretical. The community of structural biologists reacted to this phenomenon by developing and utilizing methodologies and software tools for structure model validation. The emergent focus on validation provoked us to ask: Does it have any impact on quality of new publicly available structures? We have carried out a wide range exploratory analysis of trends in relationships of pairs of factors that represent quality and features of biomacromolecules and ligands. We had two data sources for this analysis: Most data were obtained from the PDB database, while additional information concerning ligand quality was sourced from the ValidatorDB database. Some of the trends that we discovered were expected (e.g., newer structure models have, in general, higher quality than the older ones have), while other discovered trends were a surprise to us (e.g., ligand model quality is stagnant at best). The whole set of results of the exploratory analysis is available in our weekly-updated ValTrendsDB database. Users can view there all factor pair relationship plots of all trends discovered during the analysis. It is also possible to draw custom plots of any pair of factors with custom settings. Additionally, users are able to view value distribution of every factor considered. An important functionality of ValTrendsDB is the support for visualization of data points of a set of interesting PDB entries into any factor pair plot available, regardless of whether such plot is precomputed, or custom. With this functionality, users can view quality and features of their structure models of interest, e.g., structures of a journal, structures of a protein family, structures acquired using a particular experimental method, or structures assembled by specific authors, in relation to the trend across entries of the whole PDB database
ER  -

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB. In \textit{XX. setkání biochemiků a molekulárních biologů}. 2019. ISBN~978-80-210-9420-8.

Detailed Information on Publication Record