Comparative Visualization of Protein Secondary Structures

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F17%3A00095870" target="_blank" >RIV/00216224:14330/17:00095870 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1186/s12859-016-1449-z" target="_blank" >http://dx.doi.org/10.1186/s12859-016-1449-z</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12859-016-1449-z" target="_blank" >10.1186/s12859-016-1449-z</a>

Result language

angličtina

Original language name

Comparative Visualization of Protein Secondary Structures

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

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Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BMC Bioinformatics

ISSN

1471-2105

e-ISSN

—

Volume of the periodical

18

Issue of the periodical within the volume

23

Country of publishing house

GB - UNITED KINGDOM

Number of pages

12

Pages from-to

0-0

UT code for WoS article

000397487000003

EID of the result in the Scopus database

2-s2.0-85013774330