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

J. Byška, A. Jurčík, M. E. Gröller, I. Viola, B. Kozlíková

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


(Figure Presented). 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.

Original languageEnglish (US)
Pages (from-to)1-10
Number of pages10
JournalComputer Graphics Forum
Issue number3
StatePublished - Jun 1 2015
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2015 The Author(s) Computer Graphics Forum © 2015 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.


  • I.3.6 [Computer Graphics]: Picture/Image Generation - Line and curve generation

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design


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