MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids

Jan Byska, Adam Jurcik, Meister Eduard Gröller, Ivan Viola, Barbora Kozlikova
MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
Computer Graphics Forum, 3(34):1-10, May 2015. [Paper]

Information

Abstract

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.

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BibTeX

@article{Viola_Ivan_2015_MCT,
  title =      "MoleCollar and Tunnel Heat Map Visualizations for Conveying
               Spatio-Temporo-Chemical Properties Across and Along Protein
               Voids",
  author =     "Jan Byska and Adam Jurcik and Meister Eduard Gr{"o}ller and
               Ivan Viola and Barbora Kozlikova",
  year =       "2015",
  abstract =   "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.",
  month =      may,
  journal =    "Computer Graphics Forum",
  note =       "EuroVis 2015 - Conference Proceedings",
  number =     "34",
  volume =     "3",
  pages =      "1--10",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_MCT/",
}