Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations

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Authors

KOZLÍKOVÁ Barbora JURČÍK Adam BYŠKA Jan STRNAD Ondřej SOCHOR Jiří

Year of publication 2014
Type Article in Proceedings
Conference EG VCBM 2014 Eurographics Workshop on Visual Computing for Biology and Medicine
MU Faculty or unit

Faculty of Informatics

Citation
Field Informatics
Keywords protein; visualization; tunnel; animation; Voronoi diagram; Delaunay triangulation
Description Analysis and visualization of molecules and their structural features help biochemists and biologists to better understand protein behavior. Studying these structures in molecular dynamics simulations enhances this understanding. In this paper we introduce three approaches for animating specific inner pathways composed of an empty space between atoms, called tunnels. These tunnels facilitate the transport of small molecules, water solvent and ions in many proteins. They help researchers understand the structure-function relationships of proteins and the knowledge of tunnel properties improves the design of new inhibitors. Our methods are derived from selected tunnel representations when each stresses some of the important tunnel properties - width, shape, mapping of physico-chemical properties, etc. Our methods provide smooth animation of the movement of tunnels as they change their length and shape throughout the simulation.
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