J 2017

Comparative Visualization of Protein Secondary Structures

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

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 2.213

RIV identification code

RIV/00216224:14330/17:00095870

Organization unit

Faculty of Informatics

DOI

UT WoS

000397487000003

Keywords (in Czech)

komparativní vizualizace;protein;sekundární struktura

Keywords in English

comparative visualization;protein;secondary structure
Změněno: 14/6/2022 11:49, RNDr. Pavel Šmerk, Ph.D.

Abstract

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.