BYŠKA, Jan, Mathieu Le MUZIC, Eduard GRÖLLER, Ivan VIOLA and Barbora KOZLÍKOVÁ. AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. IEEE Transactions on Visualization and Computer Graphics, IEEE, 2016, vol. 22, No 1, p. 747-756. ISSN 1077-2626. doi:10.1109/TVCG.2015.2467434.
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Basic information
Original name AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
Authors BYŠKA, Jan (203 Czech Republic, belonging to the institution), Mathieu Le MUZIC (250 France), Eduard GRÖLLER (40 Austria), Ivan VIOLA (703 Slovakia) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution).
Edition IEEE Transactions on Visualization and Computer Graphics, IEEE, 2016, 1077-2626.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
Impact factor Impact factor: 2.840
RIV identification code RIV/00216224:14330/16:00089099
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1109/TVCG.2015.2467434
UT WoS 000364043400080
Keywords in English protein;aggregation;interaction;molecular dynamics;tunnel
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 2/5/2016 06:31.
Abstract
In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.
Links
MUNI/A/1206/2014, internal MU codeName: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Acronym: SKOMU)
Investor: Masaryk University, Grant Agency of Masaryk University, Category A
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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