Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Viktor Vad, Jan Byska, Adam Jurcik, Ivan Viola, Meister Eduard Gröller, Helwig Hauser, Sergio M. Margues, Jiri Damborsky, Barbora Kozlikova
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
In Eurographics Workshop on Visual Computing for Biology and Medicine 2017, pages 33-42. 2017.

Information

Abstract

The function of proteins is tightly related to their interactions with other molecules. The study of such interactions often requires to track the molecules that enter or exit specific regions of the proteins. This is investigated with molecular dynamics simulations, producing the trajectories of thousands of water molecules during hundreds of thousands of time steps. To ease the exploration of such rich spatio-temporal data, we propose a novel workflow for the analysis and visualization of large sets of water-molecule trajectories. Our solution consists of a set of visualization techniques, which help biochemists to classify, cluster, and filter the trajectories and to explore the properties and behavior of selected subsets in detail. Initially, we use an interactive histogram and a time-line visualization to give an overview of all water trajectories and select the interesting ones for further investigation. Further, we depict clusters of trajectories in a novel 2D representation illustrating the flows of water molecules. These views are interactively linked with a 3D representation where we show individual paths, including their simplification, as well as extracted statistical information displayed by isosurfaces. The proposed solution has been designed in tight collaboration with experts to support specific tasks in their scientific workflows. They also conducted several case studies to evaluate the usability and effectiveness of our new solution with respect to their research scenarios. These confirmed that our proposed solution helps in analyzing water trajectories and in extracting the essential information out of the large amount of input data.

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BibTeX

@inproceedings{vad_viktor-2017-WVE,
  title =      "Watergate: Visual Exploration of Water Trajectories in
               Protein Dynamics",
  author =     "Viktor Vad and Jan Byska and Adam Jurcik and Ivan Viola and
               Meister Eduard Gr{"o}ller and Helwig Hauser and Sergio M.
               Margues and Jiri  Damborsky and Barbora Kozlikova",
  year =       "2017",
  abstract =   "The function of proteins is tightly related to their
               interactions with other molecules. The study of such
               interactions often requires to track the molecules that
               enter or exit specific regions of the proteins. This is
               investigated with molecular dynamics simulations, producing
               the trajectories of thousands of water molecules during
               hundreds of thousands of time steps. To ease the exploration
               of such rich spatio-temporal data, we propose a novel
               workflow for the analysis and visualization of large sets of
               water-molecule trajectories. Our solution consists of a set
               of visualization techniques, which help biochemists to
               classify, cluster, and filter the trajectories and to
               explore the properties and behavior of selected subsets in
               detail. Initially, we use an interactive histogram and a
               time-line visualization to give an overview of all water
               trajectories and select the interesting ones for further
               investigation. Further, we depict clusters of trajectories
               in a novel 2D representation illustrating the flows of water
               molecules. These views are interactively linked with a 3D
               representation where we show individual paths, including
               their simplification, as well as extracted statistical
               information displayed by isosurfaces. The proposed solution
               has been designed in tight collaboration with experts to
               support specific tasks in their scientific workflows. They
               also conducted several case studies to evaluate the
               usability and effectiveness of our new solution with respect
               to their research scenarios. These confirmed that our
               proposed solution helps in analyzing water trajectories and
               in extracting the essential information out of the large
               amount of input data.",
  booktitle =  "Eurographics Workshop on Visual Computing for Biology and
               Medicine 2017",
  location =   "September, 2017 Bremen, Germany",
  pages =      "33--42",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2017/vad_viktor-2017-WVE/",
}