Comparative Visualization of Protein Secondary Structures

J 2017

Comparative Visualization of Protein Secondary Structures

KOCINCOVÁ, Lucia; Miroslava JAREŠOVÁ; Jan BYŠKA; Julius PARULEK; Helwig HAUSER et al.

Základní údaje

Originální název

Comparative Visualization of Protein Secondary Structures

Autoři

KOCINCOVÁ, Lucia; Miroslava JAREŠOVÁ; Jan BYŠKA ; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ

Vydání

BMC Bioinformatics, BioMed Central, 2017, 1471-2105

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.213

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/17:00095870

Organizační jednotka

Fakulta informatiky

Klíčová slova česky

komparativní vizualizace;protein;sekundární struktura

Klíčová slova anglicky

comparative visualization;protein;secondary structure

Změněno: 14. 6. 2022 11:49, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

Background Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. Results We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations. By introducing the information about mutual positions of protein chains into the 1D sequential representation the users are able to observe the spatial differences between the proteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely for comparison of multiple proteins or a set of time steps of molecular dynamics simulation. Conclusions The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare a set of proteins from the family of cytochromes P450 where the position of the secondary structures has a significant impact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a set of time steps our representation helps to reveal the most dynamically changing parts of the protein chain.

Citovat

KOCINCOVÁ, Lucia; Miroslava JAREŠOVÁ; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Comparative Visualization of Protein Secondary Structures. BMC Bioinformatics. BioMed Central, 2017, roč. 18, č. 23, s. 1-12. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-016-1449-z.

@article{1352179,
   author = {Kocincová, Lucia and Jarešová, Miroslava and Byška, Jan and Parulek, Julius and Hauser, Helwig and Kozlíková, Barbora},
   article_number = {23},
   doi = {https://doi.org/10.1186/s12859-016-1449-z},
   keywords = {comparative visualization;protein;secondary structure},
   language = {eng},
   issn = {1471-2105},
   journal = {BMC Bioinformatics},
   title = {Comparative Visualization of Protein Secondary Structures},
   url = {http://dx.doi.org/10.1186/s12859-016-1449-z},
   volume = {18},
   year = {2017}
}

TY  - JOUR
ID  - 1352179
AU  - Kocincová, Lucia - Jarešová, Miroslava - Byška, Jan - Parulek, Julius - Hauser, Helwig - Kozlíková, Barbora
PY  - 2017
TI  - Comparative Visualization of Protein Secondary Structures
JF  - BMC Bioinformatics
VL  - 18
IS  - 23
SP  - 1-12
EP  - 1-12
PB  - BioMed Central
SN  - 14712105
KW  - comparative visualization;protein;secondary structure
UR  - http://dx.doi.org/10.1186/s12859-016-1449-z
L2  - http://dx.doi.org/10.1186/s12859-016-1449-z
N2  - Background Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. Results We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations. By introducing the information about mutual positions of protein chains into the 1D sequential representation the users are able to observe the spatial differences between the proteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely for comparison of multiple proteins or a set of time steps of molecular dynamics simulation. Conclusions The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare a set of proteins from the family of cytochromes P450 where the position of the secondary structures has a significant impact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a set of time steps our representation helps to reveal the most dynamically changing parts of the protein chain.
ER  -

KOCINCOVÁ, Lucia; Miroslava JAREŠOVÁ; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Comparative Visualization of Protein Secondary Structures. \textit{BMC Bioinformatics}. BioMed Central, 2017, roč.~18, č.~23, s.~1-12. ISSN~1471-2105. Dostupné z: https://doi.org/10.1186/s12859-016-1449-z.

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