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.

Základní údaje

Originální název

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

Autoři

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

Vydání

ELIXIR CZ Annual Conference 2019, 2019

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

Odkazy

Conference website

Kód RIV

RIV/00216224:14740/19:00111379

Organizační jednotka

Středoevropský technologický institut

ISBN

978-80-86241-61-6

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam

Změněno: 26. 3. 2020 16:47, Mgr. Pavla Foltynová, Ph.D.

Anotace

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

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

MUNI/A/1503/2018, interní kód MU

Název: Matematické statistické modelování 3 (Akronym: MaStaMo3)

Investor: Masarykova univerzita, Matematické statistické modelování 3, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA a 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 a 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.

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