MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
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 theprotein 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 andstability 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 asmall 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 shapeof the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstractdepictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study andthe 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.
J. Byška, A. JurčíÂk, E. M. Gröller, I. Viola, and B. Kozlíková, "MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids," Computer Graphics Forum, vol. 34, iss. 3, p. 1–10, 2015. doi:10.1111/cgf.12612
[BibTeX]
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 theprotein 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 andstability 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 asmall 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 shapeof the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstractdepictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study andthe 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.
@ARTICLE {Byska2015MC,
author = "Jan By\v{s}ka and Adam Jur\v{c}\'{i}Âk and Eduard M. Gr{\"o}ller and Ivan Viola and Barbora Kozl{\'i}kov{\'a}",
title = "MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids",
journal = "Computer Graphics Forum",
year = "2015",
volume = "34",
number = "3",
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 theprotein 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 andstability 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 asmall 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 shapeof the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstractdepictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study andthe 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.",
images = "images/cgf12612-fig-0001.png",
thumbnails = "images/cgf12612-fig-0001.png",
issn = "1467-8659",
url = "//dx.doi.org/10.1111/cgf.12612",
doi = "10.1111/cgf.12612",
keywords = "Categories and Subject Descriptors (according to ACM CCS), I.3.6 [Computer Graphics]: Picture/Image Generationââ¬âLine and curve generation"
}