Interactive Exploration of Ligand Transportation through
Protein Tunnels

J 2017

Interactive Exploration of Ligand Transportation through Protein Tunnels

FURMANOVÁ, Katarína, Miroslava JAREŠOVÁ, Jan BYŠKA, Adam JURČÍK, Julius PARULEK et. al.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Změněno: 26/10/2020 18:11, RNDr. Jan Byška, Ph.D.

Abstract

V originále

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.

Citovat

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. Available from: https://dx.doi.org/10.1186/s12859-016-1448-0.

@article{1352180,
   author = {Furmanová, Katarína and Jarešová, Miroslava and Byška, Jan and Jurčík, Adam and Parulek, Julius and Hauser, Helwig and Kozlíková, Barbora},
   article_number = {22},
   doi = {http://dx.doi.org/10.1186/s12859-016-1448-0},
   keywords = {ligand transportation;protein;visualization;visual analysis},
   language = {eng},
   issn = {1471-2105},
   journal = {BMC Bioinformatics},
   title = {Interactive Exploration of Ligand Transportation through Protein Tunnels},
   url = {http://dx.doi.org/10.1186/s12859-016-1448-0},
   volume = {18},
   year = {2017}
}

TY  - JOUR
ID  - 1352180
AU  - Furmanová, Katarína - Jarešová, Miroslava - Byška, Jan - Jurčík, Adam - Parulek, Julius - Hauser, Helwig - Kozlíková, Barbora
PY  - 2017
TI  - Interactive Exploration of Ligand Transportation through Protein Tunnels
JF  - BMC Bioinformatics
VL  - 18
IS  - 22
SP  - 1-16
EP  - 1-16
PB  - BioMed Central
SN  - 14712105
KW  - ligand transportation;protein;visualization;visual analysis
UR  - http://dx.doi.org/10.1186/s12859-016-1448-0
L2  - http://dx.doi.org/10.1186/s12859-016-1448-0
N2  - 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.
ER  -

FURMANOVÁ, Katarína, Miroslava JAREŠOVÁ, Jan BYŠKA, Adam JURČÍK, Julius PARULEK, Helwig HAUSER and Barbora KOZLÍKOVÁ. Interactive Exploration of Ligand Transportation through Protein Tunnels. \textit{BMC Bioinformatics}. BioMed Central, 2017, vol.~18, No~22, p.~1-16. ISSN~1471-2105. Available from: https://dx.doi.org/10.1186/s12859-016-1448-0.

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