2DProts: database of family-wide protein secondary structure
diagrams

J 2021

2DProts: database of family-wide protein secondary structure diagrams

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Vladimír HORSKÝ, Eva HLADKÁ et. al.

Basic information

Original name

2DProts: database of family-wide protein secondary structure diagrams

Authors

HUTAŘOVÁ VAŘEKOVÁ, Ivana (203 Czech Republic, belonging to the institution), Jan HUTAŘ (203 Czech Republic, belonging to the institution), Adam MIDLIK (703 Slovakia, belonging to the institution), Vladimír HORSKÝ (203 Czech Republic, belonging to the institution), Eva HLADKÁ (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution) and Karel BERKA (203 Czech Republic)

Edition

Bioinformatics, Oxford University Press, 2021, 1367-4803

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 6.931

RIV identification code

RIV/00216224:14740/21:00122676

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/bioinformatics/btab505

UT WoS

000733374500050

Keywords in English

2DProts database; 2D diagram; proteins; database; ontologie;

Abstract

V originále

Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family’s secondary structures. 2DProts is updated weekly and is integrated into CATH.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

Citovat

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Vladimír HORSKÝ, Eva HLADKÁ, Radka SVOBODOVÁ and Karel BERKA. 2DProts: database of family-wide protein secondary structure diagrams. Bioinformatics. Oxford University Press, 2021, vol. 37, No 23, p. 4599-4601. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btab505.

@article{1799857,
   author = {Hutařová Vařeková, Ivana and Hutař, Jan and Midlik, Adam and Horský, Vladimír and Hladká, Eva and Svobodová, Radka and Berka, Karel},
   article_number = {23},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btab505},
   keywords = {2DProts database; 2D diagram; proteins; database; ontologie;},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {2DProts: database of family-wide protein secondary structure diagrams},
   url = {https://academic.oup.com/bioinformatics/article/37/23/4599/6318387},
   volume = {37},
   year = {2021}
}

TY  - JOUR
ID  - 1799857
AU  - Hutařová Vařeková, Ivana - Hutař, Jan - Midlik, Adam - Horský, Vladimír - Hladká, Eva - Svobodová, Radka - Berka, Karel
PY  - 2021
TI  - 2DProts: database of family-wide protein secondary structure diagrams
JF  - Bioinformatics
VL  - 37
IS  - 23
SP  - 4599-4601
EP  - 4599-4601
PB  - Oxford University Press
SN  - 13674803
KW  - 2DProts database
KW  - 2D diagram
KW  - proteins
KW  - database
KW  - ontologie;
UR  - https://academic.oup.com/bioinformatics/article/37/23/4599/6318387
N2  - Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family’s secondary structures. 2DProts is updated weekly and is integrated into CATH.
ER  -

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Vladimír HORSKÝ, Eva HLADKÁ, Radka SVOBODOVÁ and Karel BERKA. 2DProts: database of family-wide protein secondary structure diagrams. \textit{Bioinformatics}. Oxford University Press, 2021, vol.~37, No~23, p.~4599-4601. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btab505.

Detailed Information on Publication Record