Watergate: Visual exploration of water trajectories in protein dynamics

V. Vad, J. Byška, A. Jurčík, I. Viola, E. M. Gröller, H. Hauser, S. M. Marques, J. Damborský, B. Kozlíková

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

13 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationVCBM 2017 - Eurographics Workshop on Visual Computing for Biology and Medicine
PublisherEurographics Association
Number of pages10
ISBN (Electronic)9783038680369
StatePublished - 2017
Event2017 Eurographics Workshop on Visual Computing for Biology and Medicine, VCBM 2017 - Bremen, Germany
Duration: Sep 7 2017Sep 8 2017

Publication series

NameVCBM 2017 - Eurographics Workshop on Visual Computing for Biology and Medicine


Conference2017 Eurographics Workshop on Visual Computing for Biology and Medicine, VCBM 2017

Bibliographical note

Funding Information:
Water trajectories and the importance of their analysis has been already addressed by several research groups. Benson and Pleiss [BP14] describe a method for routing the water flow in a given direction. Very recently, the AQUA-DUCT [MMG∗16, MMG∗17] tool was released. It allows the user to extract, analyze, and visualize the behavior of solvent molecules during a molecular dynamics simulation. The visualization is currently supported by the PyMol visualization package [Sch15].

Publisher Copyright:
© 2017 The Eurographics Association.

ASJC Scopus subject areas

  • Computer Vision and Pattern Recognition
  • Biomedical Engineering


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