Visual Analysis of Biomolecular Cavities: State of the Art

Michael Krone, Barbora Kozlikova, Norbert Lindow, Marc Baaden, Daniel Baum, Julius Parulek, Hans-Christian Hege, Ivan Viola
Visual Analysis of Biomolecular Cavities: State of the Art
Computer Graphics Forum, 35(3):527-551, 2016. [paper]

Information

Abstract

In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.

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BibTeX

@article{Krone2016VABC,
  title =      "Visual Analysis of Biomolecular Cavities: State of the Art",
  author =     "Michael Krone and Barbora Kozlikova and Norbert Lindow and
               Marc Baaden and Daniel Baum and Julius Parulek and
               Hans-Christian Hege and Ivan Viola",
  year =       "2016",
  abstract =   "In this report we review and structure the branch of
               molecular visualization that is concerned with the visual
               analysis of cavities in macromolecular protein structures.
               First the necessary background, the domain terminology, and
               the goals of analytical reasoning are introduced. Based on a
               comprehensive collection of relevant research works, we
               present a novel classification for cavity detection
               approaches and structure them into four distinct classes:
               grid-based, Voronoi-based, surface-based, and probe-based
               methods. The subclasses are then formed by their
               combinations. We match these approaches with corresponding
               visualization technologies starting with direct 3D
               visualization, followed with non-spatial visualization
               techniques that for example abstract the interactions
               between structures into a relational graph, straighten the
               cavity of interest to see its profile in one view, or
               aggregate the time sequence into a single contour plot. We
               also discuss the current state of methods for the visual
               analysis of cavities in dynamic data such as molecular
               dynamics simulations. Finally, we give an overview of the
               most common tools that are actively developed and used in
               the structural biology and biochemistry research. Our report
               is concluded by an outlook on future challenges in the
               field.",
  journal =    "Computer Graphics Forum",
  number =     "3",
  volume =     "35",
  pages =      "527--551",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2016/Krone2016VABC/",
}