BYŠKA, Jan, Adam JURČÍK, Eduard M. GRÖLLER, Ivan VIOLA and Barbora KOZLÍKOVÁ. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. Computer Graphics Forum. Wiley-Blackwell, 2015, vol. 34, No 3, p. 1-10. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.12612. |
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@article{1300513, author = {Byška, Jan and Jurčík, Adam and Gröller, Eduard M. and Viola, Ivan and Kozlíková, Barbora}, article_number = {3}, doi = {http://dx.doi.org/10.1111/cgf.12612}, keywords = {protein;tunnel;heat map;molecular dynamics}, language = {eng}, issn = {0167-7055}, journal = {Computer Graphics Forum}, title = {MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids}, volume = {34}, year = {2015} }
TY - JOUR ID - 1300513 AU - Byška, Jan - Jurčík, Adam - Gröller, Eduard M. - Viola, Ivan - Kozlíková, Barbora PY - 2015 TI - MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids JF - Computer Graphics Forum VL - 34 IS - 3 SP - 1-10 EP - 1-10 PB - Wiley-Blackwell SN - 01677055 KW - protein;tunnel;heat map;molecular dynamics N2 - Studying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored and evaluated. In this paper we propose three new methods: two of them convey important properties along the long axis of a selected void during molecular dynamics and one provides a comprehensive picture across the void. The first two proposed methods use a specific heat map to present two types of information: an overview of all detected tunnels in the dynamics and their bottleneck width and stability over time, and an overview of a specific tunnel in the dynamics showing the bottleneck position and changes of the tunnel length over time. These methods help to select a small subset of tunnels, which are explored individually and in detail. For this stage we propose the third method, which shows in one static image the temporal evolvement of the shape of the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstract depictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study and the feedback from the domain experts is included. The biochemists confirmed that our novel methods help to convey the information about the appearance and properties of tunnels in a very intuitive and comprehensible manner. ER -
BYŠKA, Jan, Adam JURČÍK, Eduard M. GRÖLLER, Ivan VIOLA and Barbora KOZLÍKOVÁ. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2015, vol.~34, No~3, p.~1-10. ISSN~0167-7055. Available from: https://dx.doi.org/10.1111/cgf.12612.
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