FURMANOVÁ, Katarína, Miroslava JAREŠOVÁ, Jan BYŠKA, Adam JURČÍK, Julius PARULEK, Helwig HAUSER a Barbora KOZLÍKOVÁ. Interactive Exploration of Ligand Transportation through Protein Tunnels. BMC Bioinformatics. BioMed Central, 2017, roč. 18, č. 22, s. 1-16. ISSN 1471-2105. doi:10.1186/s12859-016-1448-0.
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Základní údaje
Originální název Interactive Exploration of Ligand Transportation through Protein Tunnels
Autoři FURMANOVÁ, Katarína (703 Slovensko, domácí), Miroslava JAREŠOVÁ (203 Česká republika, domácí), Jan BYŠKA (203 Česká republika, domácí), Adam JURČÍK (203 Česká republika, domácí), Julius PARULEK (703 Slovensko), Helwig HAUSER (40 Rakousko) a Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí).
Vydání BMC Bioinformatics, BioMed Central, 2017, 1471-2105.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10201 Computer sciences, information science, bioinformatics
Stát vydavatele Velká Británie a Severní Irsko
Utajení není předmětem státního či obchodního tajemství
WWW URL
Impakt faktor Impact factor: 2.213
Kód RIV RIV/00216224:14330/17:00095871
Organizační jednotka Fakulta informatiky
Doi http://dx.doi.org/10.1186/s12859-016-1448-0
UT WoS 000397487000002
Klíčová slova anglicky ligand transportation;protein;visualization;visual analysis
Změnil Změnil: RNDr. Jan Byška, Ph.D., učo 207879. Změněno: 26. 10. 2020 18:11.
Anotace
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.
VytisknoutZobrazeno: 19. 3. 2024 12:23