@ARTICLE {Kocincova2017SS,
author = "Kocincov{\'a}, Lucia and Jare{\v{s}}ov{\'a}, Miroslava and By{\v{s}}ka, Jan and Parulek, J{\'u}lius and Hauser, Helwig and Kozl{\'i}kov{\'a}, Barbora",
title = "Comparative visualization of protein secondary structures",
journal = "BMC Bioinformatics",
year = "2017",
volume = "18(Suppl 2)",
number = "23",
month = "feb",
abstract = "Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, anddynamic behavior. Studying these factors helps the biochemists and biologists to better understand the proteinbehavior and to design proteins with modified properties. One of the most common approaches to these studies is tocompare the protein structure with other molecules and to reveal similarities and differences in their polypeptidechains.Results: We support the comparison process by proposing a new visualization technique that bridges the gapbetween traditionally used 1D and 3D representations. By introducing the information about mutual positions ofprotein chains into the 1D sequential representation the users are able to observe the spatial differences between theproteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely forcomparison 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 aset of proteins from the family of cytochromes P450 where the position of the secondary structures has a significantimpact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a setof time steps our representation helps to reveal the most dynamically changing parts of the protein chain.",
pdf = "pdfs/Kocincova2017.pdf",
images = "images/Lucia2016Comparative.png",
thumbnails = "images/Lucia2016Comparative.png",
note = "https://doi.org/10.1186/s12859-016-1449-z"
}