Quo Vadis, Biomacromolecular Structure Quality

a 2017

Quo Vadis, Biomacromolecular Structure Quality

SVOBODOVÁ VAŘEKOVÁ, Radka, Vladimír HORSKÝ, David SEHNAL, Veronika BENDOVÁ, Lukáš PRAVDA et. al.

Basic information

Original name

Quo Vadis, Biomacromolecular Structure Quality

Authors

SVOBODOVÁ VAŘEKOVÁ, Radka, Vladimír HORSKÝ, David SEHNAL, Veronika BENDOVÁ, Lukáš PRAVDA and Jaroslav KOČA

Edition

Biophysical Society 61st Annual Meeting, New Orleans, Louisiana, 2017

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:

URL

Impact factor

Impact factor: 3.495

Organization unit

Faculty of Science

ISSN

DOI

http://dx.doi.org/10.1016/j.bpj.2016.11.1880

UT WoS

000402375600712

Keywords in English

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

Abstract

V originále

Missing answers to key questions of biomacromolecular complex structure quality motivated us to focus on an analysis of the current state of data quality and validation trends. Among others, we paid a special attention to ligand validation criteria as they are the most sensitive and interesting part of validation outputs. Our research has been based on validation data from our validation database ValidatorDB (http://ncbr.muni.cz/ValidatorDB) and PDB validation reports. Furthermore, we have compiled all these validation information into the ValTrendsDB dataabse. While certain discovered trends are very positive (e.g., clashscore markedly decreases with the year of structure publication), others are alarming (e.g., ligand quality stagnates with the year of structure publication).

Links

MUNI/A/1194/2016, interní kód MU

Name: Statistické a deterministické modelování (Acronym: StaDeMo)

Investor: Masaryk University, Category A

Citovat

SVOBODOVÁ VAŘEKOVÁ, Radka, Vladimír HORSKÝ, David SEHNAL, Veronika BENDOVÁ, Lukáš PRAVDA and Jaroslav KOČA. Quo Vadis, Biomacromolecular Structure Quality. In Biophysical Society 61st Annual Meeting, New Orleans, Louisiana. 2017. ISSN 1542-0086. Available from: https://dx.doi.org/10.1016/j.bpj.2016.11.1880.

@proceedings{1376028,
   author = {Svobodová Vařeková, Radka and Horský, Vladimír and Sehnal, David and Bendová, Veronika and Pravda, Lukáš and Koča, Jaroslav},
   booktitle = {Biophysical Society 61st Annual Meeting, New Orleans, Louisiana},
   doi = {http://dx.doi.org/10.1016/j.bpj.2016.11.1880},
   keywords = {ValTrendsDB; ValidatorDB; biomacromolecule structure quality; ligand quality; X-ray crystallography; Protein Data Bank; Validation Report; trends; interval analysis; Spearman coefficient},
   language = {eng},
   title = {Quo Vadis, Biomacromolecular Structure Quality},
   url = {http://www.cell.com/biophysj/pdf/S0006-3495(16)32910-1.pdf},
   year = {2017}
}

TY  - CONF
ID  - 1376028
AU  - Svobodová Vařeková, Radka - Horský, Vladimír - Sehnal, David - Bendová, Veronika - Pravda, Lukáš - Koča, Jaroslav
PY  - 2017
TI  - Quo Vadis, Biomacromolecular Structure Quality
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  - http://www.cell.com/biophysj/pdf/S0006-3495(16)32910-1.pdf
L2  - http://www.cell.com/biophysj/pdf/S0006-3495(16)32910-1.pdf
N2  - Missing answers to key questions of biomacromolecular complex structure quality motivated us to focus on an analysis of the current state of data quality and validation trends. Among others, we paid a special attention to ligand validation criteria as they are the most sensitive and interesting part of validation outputs. Our research has been based on validation data from our validation database ValidatorDB (http://ncbr.muni.cz/ValidatorDB) and PDB validation reports. Furthermore, we have compiled all these validation information into the ValTrendsDB dataabse. While certain discovered trends are very positive (e.g., clashscore markedly decreases with the year of structure publication), others are alarming (e.g., ligand quality stagnates with the year of structure publication).
ER  -

SVOBODOVÁ VAŘEKOVÁ, Radka, Vladimír HORSKÝ, David SEHNAL, Veronika BENDOVÁ, Lukáš PRAVDA and Jaroslav KOČA. Quo Vadis, Biomacromolecular Structure Quality. In \textit{Biophysical Society 61st Annual Meeting, New Orleans, Louisiana}. 2017. ISSN~1542-0086. Available from: https://dx.doi.org/10.1016/j.bpj.2016.11.1880.

Detailed Information on Publication Record