AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics

Jan Byska, Mathieu Le Muzic, Meister Eduard Gröller, Ivan Viola, Barbora Kozlikova
AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
IEEE Transactions on Visualization and Computer Graphics, 22(1):747-756, January 2016. [Paper]

Information

Abstract

In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.

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@article{Viola_Ivan_2015_AAM,
  title =      "AnimoAminoMiner: Exploration of Protein Tunnels and their
               Properties in Molecular Dynamics",
  author =     "Jan Byska and Mathieu Le Muzic and Meister Eduard Gr{"o}ller
               and Ivan Viola and Barbora Kozlikova",
  year =       "2016",
  abstract =   "In this paper we propose a novel method for the interactive
               exploration of protein tunnels. The basic principle of our
               approach is that we entirely abstract from the 3D/4D space
               the simulated phenomenon is embedded in. A complex 3D
               structure and its curvature information is represented only
               by a straightened tunnel centerline and its width profile.
               This representation focuses on a key aspect of the studied
               geometry and frees up graphical estate to key chemical and
               physical properties represented by surrounding amino acids.
               The method shows the detailed tunnel profile and its
               temporal aggregation. The profile is interactively linked
               with a visual overview of all amino acids which are lining
               the tunnel over time. In this overview, each amino acid is
               represented by a set of colored lines depicting the spatial
               and temporal impact of the amino acid on the corresponding
               tunnel. This representation clearly shows the importance of
               amino acids with respect to selected criteria. It helps the
               biochemists to select the candidate amino acids for mutation
               which changes the protein function in a desired way. The
               AnimoAminoMiner was designed in close cooperation with
               domain experts. Its usefulness is documented by their
               feedback and a case study, which are included.",
  month =      jan,
  issn =       "1077-2626",
  journal =    "IEEE Transactions on Visualization and Computer Graphics",
  number =     "1",
  volume =     "22",
  pages =      "747--756",
  keywords =   "aggregation, molecular dynamics, Protein, interaction,
               tunnel",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/",
}