title: Interactive exploration of ligand transportation through protein tunnels.
abstract: BACKGROUND
  Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This prevents understanding of the ligand transportation and reasoning behind its behavior along the path.
  
  
  RESULTS
  To address the needs of the domain experts we design an explorative visualization solution based on a multi-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory by exploring different attributes of the ligand and its movement, such as its distance to the active site, changes of amino acids lining the ligand, or ligand "stuckness". The process is supported by three linked views - 3D representation of the simplified trajectory, scatterplot matrix, and bar charts with line representation of ligand-lining amino acids.
  
  
  CONCLUSIONS
  The usage of our tool is demonstrated on molecular dynamics simulations provided by the domain experts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior.
authors.affiliation: Masaryk University, Brno, Czech Republic.
authors.forename: Katarína
authors.initials: K
authors.lastname: Furmanová
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: Masaryk University, Brno, Czech Republic.
authors.forename: Adam
authors.initials: A
authors.lastname: Jurčík
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: D000596:Amino Acids / Q000737:chemistry; D020134:Catalytic Domain; D007091:Image Processing, Computer-Assisted; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D008024:Ligands; D011506:Proteins
keywords: Bioinformatics visualization; Computational proteomics; Molecular visualization