@ARTICLE {Furmanova2017Ligand,
author = "Furmanov{\'a}, Katar{\'\i}na and Jare{\v{s}}ov{\'a}, Miroslava and By{\v{s}}ka, Jan and Jur{\v{c}}{\'i}k, Adam and Parulek, J{\'u}lius and Hauser, Helwig and Kozl{\'i}kov{\'a}, Barbora",
title = "Interactive exploration of ligand transportation through protein tunnels",
journal = "BMC Bioinformatics",
year = "2017",
volume = "18(Suppl 2)",
number = "22",
month = "feb",
abstract = "Background: Protein structures and their interaction with ligands have been in the focus of biochemistry andstructural biology research for decades. The transportation of ligand into the protein active site is often complexprocess, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter andimpasses. 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 amulti-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory byexploring different attributes of the ligand and its movement, such as its distance to the active site, changes of aminoacids lining the ligand, or ligand “stuckness�. The process is supported by three linked views – 3D representation of thesimplified 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 domainexperts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps tonavigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior",
pdf = "pdfs/Furmanova2017.pdf",
images = "images/Furmanova2016Interactive.png",
thumbnails = "images/Furmanova2016Interactive.png",
note = "https://doi.org/10.1186/s12859-016-1448-0"
}