Bringing validation information closer to the user

k 2018

Bringing validation information closer to the user

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ et. al.

Základní údaje

Originální název

Bringing validation information closer to the user

Autoři

SMART, Oliver S. (826 Velká Británie a Severní Irsko), Vladimír HORSKÝ (203 Česká republika, garant, domácí), Swanand GORE (826 Velká Británie a Severní Irsko), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí), Veronika BENDOVÁ (203 Česká republika, domácí), Gerard J. KLEYWEGT (528 Nizozemské království) a Sameer VELANKAR (826 Velká Británie a Severní Irsko)

Vydání

CEITEC PhD and Postdoc Retreat 2018, 2018

Další údaje

Jazyk

angličtina

Typ výsledku

Prezentace na konferencích

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14740/18:00102640

Organizační jednotka

Středoevropský technologický institut

ISBN

978-80-210-8941-9

Klíčová slova anglicky

PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB

Štítky

rivok

Příznaky

Mezinárodní význam

Změněno: 29. 4. 2018 17:17, Mgr. Vladimír Horský, Ph.D.

Anotace

V originále

Universal availability of biomacromolecular structural data has gradually changed life sciences. Various databases, the most prominent being the Protein Data Bank (PDB), enable access to plethora of published structures. Unfortunately, questions regarding quality of structure models have increased in importance in recent years. Therefore, all new structures are validated at the time of their submission to PDB. Here, we show how values of available validation metrics can be combined into an overall score that enables ranking of macromolecular structures and their domains in search results. This solution brings validation information closer to the general scientific community. A big challenge of crystallographic studies is how to correctly interpret electron density that is present in the binding site. It either represents an expected ligand, or just solvent molecules. As a result, ligand model quality in the PDB database was and still remains a concerning matter. That is why several ligand validation methods have been integrated into the PDB validation pipeline. Here, we describe these methods, along with our finding that the currently used LLDF metric can give misleading results.

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

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT a Sameer VELANKAR. Bringing validation information closer to the user. In CEITEC PhD and Postdoc Retreat 2018. 2018. ISBN 978-80-210-8941-9.

@proceedings{1415496,
   author = {Smart, Oliver S. and Horský, Vladimír and Gore, Swanand and Svobodová Vařeková, Radka and Bendová, Veronika and Kleywegt, Gerard J. and Velankar, Sameer},
   booktitle = {CEITEC PhD and Postdoc Retreat 2018},
   keywords = {PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; ligands; ValTrendsDB},
   language = {eng},
   isbn = {978-80-210-8941-9},
   title = {Bringing validation information closer to the user},
   year = {2018}
}

TY  - CONF
ID  - 1415496
AU  - Smart, Oliver S. - Horský, Vladimír - Gore, Swanand - Svobodová Vařeková, Radka - Bendová, Veronika - Kleywegt, Gerard J. - Velankar, Sameer
PY  - 2018
TI  - Bringing validation information closer to the user
SN  - 9788021089419
KW  - PDB
KW  - Protein Data Bank
KW  - three-dimensional macromolecular structure
KW  - validation
KW  - ligands
KW  - ValTrendsDB
N2  - Universal availability of biomacromolecular structural data has gradually changed life sciences. Various databases, the most prominent being the Protein Data Bank (PDB), enable access to plethora of published structures. Unfortunately, questions regarding quality of structure models have increased in importance in recent years. Therefore, all new structures are validated at the time of their submission to PDB. Here, we show how values of available validation metrics can be combined into an overall score that enables ranking of macromolecular structures and their domains in search results. This solution brings validation information closer to the general scientific community. A big challenge of crystallographic studies is how to correctly interpret electron density that is present in the binding site. It either represents an expected ligand, or just solvent molecules. As a result, ligand model quality in the PDB database was and still remains a concerning matter. That is why several ligand validation methods have been integrated into the PDB validation pipeline. Here, we describe these methods, along with our finding that the currently used LLDF metric can give misleading results.
ER  -

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT a Sameer VELANKAR. Bringing validation information closer to the user. In \textit{CEITEC PhD and Postdoc Retreat 2018}. 2018. ISBN~978-80-210-8941-9.

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