KRONE, Michael, Barbora KOZLÍKOVÁ, Norbert LINDOW, Marc BAADEN, Daniel BAUM, Julius PARULEK, Hans-Christian HEGE and Ivan VIOLA. Visual Analysis of Biomolecular Cavities: State of the Art. Computer Graphics Forum, The Eurographics Association and John Wiley & Sons Ltd., 2016, vol. 35, No 3, p. 527-551. ISSN 0167-7055. doi:10.1111/cgf.12928.
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Basic information
Original name Visual Analysis of Biomolecular Cavities: State of the Art
Authors KRONE, Michael (276 Germany), Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution), Norbert LINDOW (276 Germany), Marc BAADEN (250 France), Daniel BAUM (276 Germany), Julius PARULEK (703 Slovakia), Hans-Christian HEGE (276 Germany) and Ivan VIOLA (703 Slovakia).
Edition Computer Graphics Forum, The Eurographics Association and John Wiley & Sons Ltd. 2016, 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: 1.611
RIV identification code RIV/00216224:14330/16:00090248
Organization unit Faculty of Informatics
UT WoS 000379912300054
Keywords in English biomolecules;visualization;visual analysis;cavity
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 27/4/2017 05:56.
In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.
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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