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J. Byska, M. Le Muzic, E. Gröller, I. Viola, B. Kozlikova:
"AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics";
Poster: Symposium on Biological Data Visualization (BioVis) at ISMB 2017, Prag (eingeladen); 24.07.2017; in: "Proceedings of the Symposium on Biological Data Visualization (BioVis) at ISMB 2017", (2017), S. 1 - 10.

Protein structures have been in the focus of structural biology research for decades. The study of their interactions with other smaller molecules (known as ligands) helps to reveal the fundamentals of biochemical processes that are taking place in living cells. Such reaction between a protein and a ligand often takes place deep inside the protein structure. In this paper, we present a novel visualization method for interactive exploration of protein tunnels, which connect the protein surface with deeply buried reaction sites. The tunnel geometry together with biochemical properties of surrounding amino acids and their changes over time determine whether a ligand can pass through the tunnel and reach the reaction site. The proposed visualization abstracts from the common 3D tunnel representation. The complex geometry of a tunnel is simplified by straightening the tunnel and depicting only its width profile and its changes over time. This frees up the visual space and allows the expert to directly depict the key physico-chemical properties of individual amino acids surrounding the tunnel in a single view. In our representation, each amino acid is depicted as a set of colored lines showing the spatial and temporal impact of the amino acid on the tunnel. The vertical ordering communicates the importance of amino acids with respect to selected criteria. It helps biochemists to select the most interesting candidates for further examination. The representation was developed in tight collaboration with domain experts and their feedback is presented on case studies.

http://dx.doi.org/10.1109/TVCG.2015.2467434

http://publik.tuwien.ac.at/files/publik_264276.pdf