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. doi:10.1186/s12859-016-1449-z.
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Základní údaje
Originální název Comparative Visualization of Protein Secondary Structures
Autoři KOCINCOVÁ, Lucia (703 Slovensko, domácí), Miroslava JAREŠOVÁ (203 Česká republika, domácí), Jan BYŠKA (203 Česká republika, domácí), Julius PARULEK (703 Slovensko), Helwig HAUSER (40 Rakousko) a Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí).
Vydání BMC Bioinformatics, BioMed Central, 2017, 1471-2105.
Další údaje
Originální 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
WWW URL
Impakt faktor Impact factor: 2.213
Kód RIV RIV/00216224:14330/17:00095870
Organizační jednotka Fakulta informatiky
Doi http://dx.doi.org/10.1186/s12859-016-1449-z
UT WoS 000397487000003
Klíčová slova česky komparativní vizualizace;protein;sekundární struktura
Klíčová slova anglicky comparative visualization;protein;secondary structure
Změnil Změnil: RNDr. Pavel Šmerk, Ph.D., učo 3880. Změněno: 14. 6. 2022 11:49.
Anotace
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.
VytisknoutZobrazeno: 19. 3. 2024 10:55