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.

Základní údaje

Originální název

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

Autoři

HUTAŘOVÁ VAŘEKOVÁ, Ivana (203 Česká republika, domácí), Jan HUTAŘ (203 Česká republika, domácí), Adam MIDLIK (703 Slovensko, domácí), Vladimír HORSKÝ (203 Česká republika, domácí), Eva HLADKÁ (203 Česká republika, domácí), Radka SVOBODOVÁ (203 Česká republika, garant, domácí) a Karel BERKA (203 Česká republika)

Vydání

Bioinformatics, Oxford University Press, 2021, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.931

Kód RIV

RIV/00216224:14740/21:00122676

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000733374500050

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 2. 2022 15:23, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

EF16_013/0001777, projekt VaV

Název: ELIXIR-CZ: Budování kapacit

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

Citovat

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Vladimír HORSKÝ, Eva HLADKÁ, Radka SVOBODOVÁ a Karel BERKA. 2DProts: database of family-wide protein secondary structure diagrams. Bioinformatics. Oxford University Press, 2021, roč. 37, č. 23, s. 4599-4601. ISSN 1367-4803. Dostupné z: 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 a Karel BERKA. 2DProts: database of family-wide protein secondary structure diagrams. \textit{Bioinformatics}. Oxford University Press, 2021, roč.~37, č.~23, s.~4599-4601. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btab505.

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