Family-wide annotation and schematic 2D visualization of
secondary structure elements

k 2018

Family-wide annotation and schematic 2D visualization of secondary structure elements

SVOBODOVÁ VAŘEKOVÁ, Radka, Ivana HUTAŘOVÁ VAŘEKOVÁ, Adam MIDLIK, Jan HUTAŘ, Tarakaramji MOTURU et. al.

Basic information

Original name

Family-wide annotation and schematic 2D visualization of secondary structure elements

Authors

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

Edition

National Bioinformatic Conference ENBIK, 2018

Other information

Language

English

Type of outcome

Prezentace na konferencích

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Organization unit

Faculty of Science

Změněno: 22/1/2020 13:12, Mgr. et Mgr. Adam Midlik, Ph.D.

Abstract

V originále

Large amount of structural data is available about individual protein families originating from different organisms, binding various ligands and containing diverse mutations. Secondary structure elements (SSEs) are often characteristic for a protein family and participate in the formation of protein fold. Composition and organization of SSEs can help to identify similarities and differences between proteins within protein families. To utilize the SSEs for research on protein families, we should be able to easily and automatically link and intercompare corresponding SSEs within one protein family. Specifically, the corresponding SSEs should have the same name (annotation) and we need a transparent and coherent schema of their localization in the protein structures, retaining structural information (i.e., minimize a deviation between SSEs distances in 2D schema and in 3D structure). We developed a tool set [1] fulfilling these requirements. It was successfully tested on all CATH families and its utilization in Protein Data Bank and CATH is planned. [1] Svobodová Vařeková, R., Midlik, A., Hutařová Vařeková, I., Hutař, J., Navrátilová, V., Koča, J., Berka, K. (2018). Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. Biophys J, 114(3), 46a-47a.

Citovat

SVOBODOVÁ VAŘEKOVÁ, Radka, Ivana HUTAŘOVÁ VAŘEKOVÁ, Adam MIDLIK, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Jaroslav KOČA and Karel BERKA. Family-wide annotation and schematic 2D visualization of secondary structure elements. In National Bioinformatic Conference ENBIK. 2018.

@proceedings{1608457,
   author = {Svobodová Vařeková, Radka and Hutařová Vařeková, Ivana and Midlik, Adam and Hutař, Jan and Moturu, Tarakaramji and Navrátilová, Veronika and Koča, Jaroslav and Berka, Karel},
   booktitle = {National Bioinformatic Conference ENBIK},
   language = {eng},
   title = {Family-wide annotation and schematic 2D visualization of secondary structure elements},
   url = {http://www.enbik.cz/enbik2018/},
   year = {2018}
}

TY  - CONF
ID  - 1608457
AU  - Svobodová Vařeková, Radka - Hutařová Vařeková, Ivana - Midlik, Adam - Hutař, Jan - Moturu, Tarakaramji - Navrátilová, Veronika - Koča, Jaroslav - Berka, Karel
PY  - 2018
TI  - Family-wide annotation and schematic 2D visualization of secondary structure elements
UR  - http://www.enbik.cz/enbik2018/
N2  - Large amount of structural data is available about individual protein families originating from different organisms, binding various ligands and containing diverse mutations. Secondary structure elements (SSEs) are often characteristic for a protein family and participate in the formation of protein fold. Composition and organization of SSEs can help to identify similarities and differences between proteins within protein families. To utilize the SSEs for research on protein families, we should be able to easily and automatically link and intercompare corresponding SSEs within one protein family. Specifically, the corresponding SSEs should have the same name (annotation) and we need a transparent and coherent schema of their localization in the protein structures, retaining structural information (i.e., minimize a deviation between SSEs distances in 2D schema and in 3D structure). We developed a tool set [1] fulfilling these requirements. It was successfully tested on all CATH families and its utilization in Protein Data Bank and CATH is planned. [1] Svobodová Vařeková, R., Midlik, A., Hutařová Vařeková, I., Hutař, J., Navrátilová, V., Koča, J., Berka, K. (2018). Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. Biophys J, 114(3), 46a-47a.
ER  -

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