Automated family-wide annotation of secondary structure
elements

C 2019

Automated family-wide annotation of secondary structure elements

MIDLIK, Adam; Ivana HUTAŘOVÁ VAŘEKOVÁ; Jan HUTAŘ; Tarakaramji MOTURU; Veronika NAVRÁTILOVÁ et al.

Základní údaje

Originální název

Automated family-wide annotation of secondary structure elements

Autoři

MIDLIK, Adam; Ivana HUTAŘOVÁ VAŘEKOVÁ ; Jan HUTAŘ; Tarakaramji MOTURU; Veronika NAVRÁTILOVÁ; Jaroslav KOČA; Karel BERKA a Radka SVOBODOVÁ VAŘEKOVÁ

Vydání

Second Edition. New York, Protein supersecondary structures: Methods and protocols, od s. 47-71, 25 s. Methods in Molecular Biology, 2019

Nakladatel

Humana Press

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/19:00109647

Organizační jednotka

Středoevropský technologický institut

ISBN

978-1-4939-9160-0

Klíčová slova anglicky

Annotation; Secondary structure; Secondary structure elements; Protein family; Protein domain; SecStrAnnotator; Structural alignment; Secondary structure assignment

Štítky

143160, rivok

Příznaky

Mezinárodní význam

Změněno: 23. 1. 2022 19:59, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability. This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.

Návaznosti

EF16_013/0001777, projekt VaV

Název: ELIXIR-CZ: Budování kapacit

LM2015047, 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

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

676559, interní kód MU

Název: ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences (Akronym: ELIXIR-EXCELERATE)

Investor: Evropská unie, ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences, RI Research Infrastructures (Excellent Science)

Citovat

MIDLIK, Adam; Ivana HUTAŘOVÁ VAŘEKOVÁ; Jan HUTAŘ; Tarakaramji MOTURU; Veronika NAVRÁTILOVÁ; Jaroslav KOČA; Karel BERKA a Radka SVOBODOVÁ VAŘEKOVÁ. Automated family-wide annotation of secondary structure elements. In Alexander E. Kister. Protein supersecondary structures: Methods and protocols. Second Edition. New York: Humana Press, 2019, s. 47-71. Methods in Molecular Biology. ISBN 978-1-4939-9160-0. Dostupné z: https://doi.org/10.1007/978-1-4939-9161-7_3.

@inbook{1530759,
   author = {Midlik, Adam and Hutařová Vařeková, Ivana and Hutař, Jan and Moturu, Tarakaramji and Navrátilová, Veronika and Koča, Jaroslav and Berka, Karel and Svobodová Vařeková, Radka},
   address = {New York},
   booktitle = {Protein supersecondary structures: Methods and protocols},
   doi = {https://doi.org/10.1007/978-1-4939-9161-7_3},
   edition = {Second Edition},
   editor = {Alexander E. Kister},
   keywords = {Annotation; Secondary structure; Secondary structure elements; Protein family; Protein domain; SecStrAnnotator; Structural alignment; Secondary structure assignment},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York},
   isbn = {978-1-4939-9160-0},
   pages = {47-71},
   publisher = {Humana Press},
   title = {Automated family-wide annotation of secondary structure elements},
   url = {https://link.springer.com/protocol/10.1007/978-1-4939-9161-7_3},
   year = {2019}
}

TY  - CHAP
ID  - 1530759
AU  - Midlik, Adam - Hutařová Vařeková, Ivana - Hutař, Jan - Moturu, Tarakaramji - Navrátilová, Veronika - Koča, Jaroslav - Berka, Karel - Svobodová Vařeková, Radka
PY  - 2019
TI  - Automated family-wide annotation of secondary structure elements
VL  - Methods in Molecular Biology
PB  - Humana Press
CY  - New York
SN  - 9781493991600
KW  - Annotation
KW  - Secondary structure
KW  - Secondary structure elements
KW  - Protein family
KW  - Protein domain
KW  - SecStrAnnotator
KW  - Structural alignment
KW  - Secondary structure assignment
UR  - https://link.springer.com/protocol/10.1007/978-1-4939-9161-7_3
L2  - https://link.springer.com/protocol/10.1007/978-1-4939-9161-7_3
N2  - Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability. This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.
ER  -

MIDLIK, Adam; Ivana HUTAŘOVÁ VAŘEKOVÁ; Jan HUTAŘ; Tarakaramji MOTURU; Veronika NAVRÁTILOVÁ; Jaroslav KOČA; Karel BERKA a Radka SVOBODOVÁ VAŘEKOVÁ. Automated family-wide annotation of secondary structure elements. In Alexander E. Kister. \textit{Protein supersecondary structures: Methods and protocols}. Second Edition. New York: Humana Press, 2019, s.~47-71. Methods in Molecular Biology. ISBN~978-1-4939-9160-0. Dostupné z: https://doi.org/10.1007/978-1-4939-9161-7\_{}3.

Přehled o publikaci