KOCINCOVÁ, Lucia, Miroslava JAREŠOVÁ, Jan BYŠKA, Julius PARULEK, Helwig HAUSER and Barbora KOZLÍKOVÁ. Comparative Visualization of Protein Secondary Structures. BMC Bioinformatics, BioMed Central, 2017, vol. 18, No 23, p. 0-0. ISSN 1471-2105. doi:10.1186/s12859-016-1449-z.
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Basic information
Original name Comparative Visualization of Protein Secondary Structures
Authors KOCINCOVÁ, Lucia (703 Slovakia, belonging to the institution), Miroslava JAREŠOVÁ (203 Czech Republic, belonging to the institution), Jan BYŠKA (203 Czech Republic, belonging to the institution), Julius PARULEK (703 Slovakia), Helwig HAUSER (40 Austria) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution).
Edition BMC Bioinformatics, BioMed Central, 2017, 1471-2105.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 2.213
RIV identification code RIV/00216224:14330/17:00095870
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1186/s12859-016-1449-z
UT WoS 000397487000003
Keywords (in Czech) komparativní vizualizace;protein;sekundární struktura
Keywords in English comparative visualization;protein;secondary structure
Changed by Changed by: RNDr. Jan Byška, Ph.D., učo 207879. Changed: 26/10/2020 18:03.
Abstract
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.
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