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Comparative Visualization of Protein Secondary Structures

Lucia Kocincova, Miroslava Jaresova, Jan Byska, Julius Parulek, Helwig Hauser, Barbora Kozlikova

INPROCEEDINGS, BMC Bioinformatics, October, 2016

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 case studies. The first study 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 study 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.

Published

BMC Bioinformatics

  • Pages: –
  • Date: October 2016
  • Project: physioillustration

Media

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BibTeX

@inproceedings{Lucia2016Comparative,
 author={Lucia Kocincova and Miroslava Jaresova and Jan Byska and Julius Parulek and 
 Helwig Hauser and Barbora Kozlikova},
 booktitle={BMC Bioinformatics},
 title={Comparative Visualization of Protein Secondary Structures},
 year={2016},
 month={October},
 pages={--}, 
 keywords={Molecular Visualization; Molecular Sequence Analysis; Molecular Structure and
 Function},
 doi={--}, 
 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 case studies. The first
 study 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 study 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.},



}






 Last Modified: Jean-Paul Balabanian, 2017-06-30