ValTrendsDB: Enabling comparison of quality and features of
biomacromolecular complexes to the global trend

a 2019

ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend

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

Basic information

Original name

ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend

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

ELIXIR CZ Annual Conference 2019, 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/00216224:14740/19:00111379

Organization unit

Central European Institute of Technology

ISBN

978-80-86241-61-6

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

Models of biomacromolecules are assembled from experimentally measured data, which can invite errors. Some structure models were found to be erroneous to the point of retracting articles with conclusions based on these models. The community began developing and using methodologies for validation of structure models. This focus of quality had us wondering whether it has any impact on quality of newer structures. To provide food for thought regarding this inquiry (and several others), 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. Data from the PDB database, as well as our own ValidatorDB database that contains ligand validation information, have been transformed into 88 factors for the analysis. We expected some of the discovered trends (e.g., newer structures have better quality), while others surprised us (e.g., ligand quality is stagnant at best). Complete results of our analysis are available in the weekly updated ValTrendsDB database (ncbr.muni.cz/ValTrendsDB). Users of the database can view factor-pair plots of all explored relationships, including those that provided us with interesting trends. An important functionality of ValTrendsDB is visualization of data points, which represent one or more PDB entries, into factor-pair plots served by the database as results of the exploratory analysis. This way, users can compare quality and features of their structure(s) of interest to the trends across 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. ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

@proceedings{1581337,
   author = {Horský, Vladimír and Bendová, Veronika and Toušek, Dominik and Koča, Jaroslav and Svobodová Vařeková, Radka},
   booktitle = {ELIXIR CZ Annual Conference 2019},
   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 = {978-80-86241-61-6},
   title = {ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend},
   url = {https://www.elixir-czech.cz/events/elixir-cz-annual-conference-nov-2019},
   year = {2019}
}

TY  - CONF
ID  - 1581337
AU  - Horský, Vladimír - Bendová, Veronika - Toušek, Dominik - Koča, Jaroslav - Svobodová Vařeková, Radka
PY  - 2019
TI  - ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend
SN  - 9788086241616
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://www.elixir-czech.cz/events/elixir-cz-annual-conference-nov-2019
L2  - https://www.elixir-czech.cz/events/elixir-cz-annual-conference-nov-2019
N2  - Models of biomacromolecules are assembled from experimentally measured data, which can invite errors. Some structure models were found to be erroneous to the point of retracting articles with conclusions based on these models. The community began developing and using methodologies for validation of structure models. This focus of quality had us wondering whether it has any impact on quality of newer structures. To provide food for thought regarding this inquiry (and several others), 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. Data from the PDB database, as well as our own ValidatorDB database that contains ligand validation information, have been transformed into 88 factors for the analysis. We expected some of the discovered trends (e.g., newer structures have better quality), while others surprised us (e.g., ligand quality is stagnant at best). Complete results of our analysis are available in the weekly updated ValTrendsDB database (ncbr.muni.cz/ValTrendsDB). Users of the database can view factor-pair plots of all explored relationships, including those that provided us with interesting trends. An important functionality of ValTrendsDB is visualization of data points, which represent one or more PDB entries, into factor-pair plots served by the database as results of the exploratory analysis. This way, users can compare quality and features of their structure(s) of interest to the trends across the whole PDB database
ER  -

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend. In \textit{ELIXIR CZ Annual Conference 2019}. 2019. ISBN~978-80-86241-61-6.

Detailed Information on Publication Record