FURMANOVÁ, Katarína, Miroslava JAREŠOVÁ, Jan BYŠKA, Adam JURČÍK, Julius PARULEK, Helwig HAUSER and Barbora KOZLÍKOVÁ. Interactive Exploration of Ligand Transportation through Protein Tunnels. BMC Bioinformatics, BioMed Central, 2017, vol. 18, No 22, p. 1-16. ISSN 1471-2105. doi:10.1186/s12859-016-1448-0.
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Basic information
Original name Interactive Exploration of Ligand Transportation through Protein Tunnels
Authors FURMANOVÁ, Katarína (703 Slovakia, belonging to the institution), Miroslava JAREŠOVÁ (203 Czech Republic, belonging to the institution), Jan BYŠKA (203 Czech Republic, belonging to the institution), Adam JURČÍK (203 Czech Republic, belonging to the institution), Julius PARULEK (703 Slovakia), Helwig HAUSER (40 Austria) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution).
Edition BMC Bioinformatics, BioMed Central, 2017, 1471-2105.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 2.213
RIV identification code RIV/00216224:14330/17:00095871
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1186/s12859-016-1448-0
UT WoS 000397487000002
Keywords in English ligand transportation;protein;visualization;visual analysis
Changed by Changed by: RNDr. Jan Byška, Ph.D., učo 207879. Changed: 26/10/2020 18:11.
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.
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