BYŠKA, Jan, Adam JURČÍK, Eduard M. GRÖLLER, Ivan VIOLA and Barbora KOZLÍKOVÁ. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. Computer Graphics Forum, Wiley-Blackwell, 2015, vol. 34, No 3, p. 1-10. ISSN 0167-7055. doi:10.1111/cgf.12612.
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Basic information
Original name MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
Authors BYŠKA, Jan (203 Czech Republic, belonging to the institution), Adam JURČÍK (203 Czech Republic, belonging to the institution), Eduard M. GRÖLLER (40 Austria), Ivan VIOLA (703 Slovakia) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution).
Edition Computer Graphics Forum, Wiley-Blackwell, 2015, 0167-7055.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher Switzerland
Confidentiality degree is not subject to a state or trade secret
Impact factor Impact factor: 1.542
RIV identification code RIV/00216224:14330/15:00083057
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1111/cgf.12612
UT WoS 000358328200003
Keywords in English protein;tunnel;heat map;molecular dynamics
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 2/5/2016 06:09.
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.
Links
7AMB15AT018, research and development projectName: Vizualizace a interaktivní prozkoumávání dynamického chování velkých molekulárních systémů
Investor: Ministry of Education, Youth and Sports of the CR, Mobility Activity
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