Jan Byska, Adam Jurcik, 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
- Publication Type: Journal Paper with Conference Talk
- Workgroup(s)/Project(s):
- Date: May 2015
- Journal: Computer Graphics Forum
- Volume: 3
- Number: 34
- Note: EuroVis 2015 - Conference Proceedings
- Location: Cagliari, Italy
- Lecturer: Jan Byska
- Event: Eurographics Conference on Visualization (EuroVis) (2015)
- Conference date: 25. May 2015 – 29. May 2015
- Pages: 1 – 10
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.Additional Files and Images
Weblinks
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 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",
volume = "3",
number = "34",
note = "EuroVis 2015 - Conference Proceedings",
pages = "1--10",
URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_MCT/",
}