Do trends in biomacromolecular structure quality inspire
optimism?

a 2017

Do trends in biomacromolecular structure quality inspire optimism?

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Sameer VELANKAR, Jaroslav KOČA et. al.

Základní údaje

Originální název

Do trends in biomacromolecular structure quality inspire optimism?

Autoři

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

Vydání

25th Conference on Intelligent Systems for Molecular Biology (ISMB) / 16th Conference on European Conference on Computational Biology (ECCB) 2017, 2017

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

ValTrendsDB; ValidatorDB; biomacromolecule structure quality; ligand quality; X-ray crystallography; Protein Data Bank; Validation Report; trends; interval analysis; Spearman coefficient

Příznaky

Mezinárodní význam

Změněno: 14. 3. 2018 11:11, doc. RNDr. Radka Svobodová, Ph.D.

Anotace

V originále

A wide scale analysis of trends in size and quality of biomacromolecules and their ligands has been performed. 88 factors that quantified quality and metadata properties of biomacromolecular complexes have been considered. Source data for the analysis came from the Protein Data Bank database. The state of quality of ligands was sourced from the ValidatorDB database that was developed by our team. Some discovered trends were expected to exist (e.g., newer structures have better quality). Other trends came as a surprise to us (e.g., ligand quality is stagnant at best, currently utilised structure validation methods do not validate ligands well). All trends that have been discovered in the analysis are openly available in the ValTrendsDB database.

Návaznosti

MUNI/A/1194/2016, interní kód MU

Název: Statistické a deterministické modelování (Akronym: StaDeMo)

Investor: Masarykova univerzita, Statistické a deterministické modelování, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Sameer VELANKAR a Jaroslav KOČA. Do trends in biomacromolecular structure quality inspire optimism? In 25th Conference on Intelligent Systems for Molecular Biology (ISMB) / 16th Conference on European Conference on Computational Biology (ECCB) 2017. 2017.

@proceedings{1385957,
   author = {Horský, Vladimír and Bendová, Veronika and Svobodová Vařeková, Radka and Velankar, Sameer and Koča, Jaroslav},
   booktitle = {25th Conference on Intelligent Systems for Molecular Biology (ISMB) / 16th Conference on European Conference on Computational Biology (ECCB) 2017},
   keywords = {ValTrendsDB; ValidatorDB; biomacromolecule structure quality; ligand quality; X-ray crystallography; Protein Data Bank; Validation Report; trends; interval analysis; Spearman coefficient},
   language = {eng},
   title = {Do trends in biomacromolecular structure quality inspire optimism?},
   url = {https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=A},
   year = {2017}
}

TY  - CONF
ID  - 1385957
AU  - Horský, Vladimír - Bendová, Veronika - Svobodová Vařeková, Radka - Velankar, Sameer - Koča, Jaroslav
PY  - 2017
TI  - Do trends in biomacromolecular structure quality inspire optimism?
KW  - ValTrendsDB
KW  - ValidatorDB
KW  - biomacromolecule structure quality
KW  - ligand quality
KW  - X-ray crystallography
KW  - Protein Data Bank
KW  - Validation Report
KW  - trends
KW  - interval analysis
KW  - Spearman coefficient
UR  - https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=A
L2  - https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=A
N2  - A wide scale analysis of trends in size and quality of biomacromolecules and their ligands has been performed. 88 factors that quantified quality and metadata properties of biomacromolecular complexes have been considered. Source data for the analysis came from the Protein Data Bank database. The state of quality of ligands was sourced from the ValidatorDB database that was developed by our team. Some discovered trends were expected to exist (e.g., newer structures have better quality). Other trends came as a surprise to us (e.g., ligand quality is stagnant at best, currently utilised structure validation methods do not validate ligands well). All trends that have been discovered in the analysis are openly available in the ValTrendsDB database.
ER  -

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Sameer VELANKAR a Jaroslav KOČA. Do trends in biomacromolecular structure quality inspire optimism? In \textit{25th Conference on Intelligent Systems for Molecular Biology (ISMB) / 16th Conference on European Conference on Computational Biology (ECCB) 2017}. 2017.

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