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Interactive Exploration of Ligand Transportation through Protein Tunnels

Katararina Furmanova, Miroslava Jaresova, Jan Byska, Adam Jurcik , Julius Parulek, Helwig Hauser, Barbora Kozlikova

INPROCEEDINGS, BMC Bioinformatics, October, 2016

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 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 simulation 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

Published

BMC Bioinformatics

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

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BibTeX

@inproceedings{Furmanova2016Interactive,
 author={Katararina Furmanova and Miroslava Jaresova and Jan Byska and Adam Jurcik 
 and Julius Parulek and Helwig Hauser and Barbora Kozlikova},
 booktitle={BMC Bioinformatics},
 title={Interactive Exploration of Ligand Transportation through Protein Tunnels},
 year={2016},
 month={October},
 pages={--}, 
 keywords={Molecular Visualization; Bioinformatics Visualization; Computational
 Proteomics},
 doi={--}, 
 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 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 simulation
 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},



}






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