title: Comparative visualization of protein secondary structures.
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.
authors.affiliation: Masaryk University, Brno, Czech Republic.
authors.forename: Lucia
authors.initials: L
authors.lastname: Kocincová
authors.affiliation: Masaryk University, Brno, Czech Republic.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Jarešová
authors.affiliation: Masaryk University, Brno, Czech Republic. jan.byska@gmail.com.|University of Bergen, Bergen, Norway. jan.byska@gmail.com.
authors.forename: Jan
authors.initials: J
authors.lastname: Byška
authors.affiliation: University of Bergen, Bergen, Norway.
authors.forename: Július
authors.initials: J
authors.lastname: Parulek
authors.affiliation: University of Bergen, Bergen, Norway.
authors.forename: Helwig
authors.initials: H
authors.lastname: Hauser
authors.affiliation: Masaryk University, Brno, Czech Republic.
authors.forename: Barbora
authors.initials: B
authors.lastname: Kozlíková
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment
chemical_list: D011506:Proteins
keywords: Molecular sequence analysis; Molecular structure and function; Molecular visualization