AnimoAminoMiner: Exploration of Protein Tunnels and their
Properties in Molecular Dynamics

J 2016

AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics

BYŠKA, Jan; Mathieu Le MUZIC; Eduard GRÖLLER; Ivan VIOLA; Barbora KOZLÍKOVÁ et. al.

Základní údaje

Originální název

AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics

Autoři

BYŠKA, Jan (203 Česká republika, domácí); Mathieu Le MUZIC (250 Francie); Eduard GRÖLLER (40 Rakousko); Ivan VIOLA (703 Slovensko) a Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí)

Vydání

IEEE Transactions on Visualization and Computer Graphics, IEEE, 2016, 1077-2626

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.840

Kód RIV

RIV/00216224:14330/16:00089099

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1109/TVCG.2015.2467434

UT WoS

000364043400080

EID Scopus

2-s2.0-84946606231

Klíčová slova anglicky

protein;aggregation;interaction;molecular dynamics;tunnel

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 5. 2016 06:31, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

MUNI/A/1206/2014, interní kód MU

Název: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Akronym: SKOMU)

Investor: Masarykova univerzita, Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

7AMB15AT018, projekt VaV

Název: Vizualizace a interaktivní prozkoumávání dynamického chování velkých molekulárních systémů

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Vizualizace a interaktivní prozkoumávání dynamického chování velkých molekulárních systémů

Citovat

BYŠKA, Jan; Mathieu Le MUZIC; Eduard GRÖLLER; Ivan VIOLA a Barbora KOZLÍKOVÁ. AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2016, roč. 22, č. 1, s. 747-756. ISSN 1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2015.2467434.

@article{1309622,
   author = {Byška, Jan and Muzic, Mathieu Le and Gröller, Eduard and Viola, Ivan and Kozlíková, Barbora},
   article_number = {1},
   doi = {http://dx.doi.org/10.1109/TVCG.2015.2467434},
   keywords = {protein;aggregation;interaction;molecular dynamics;tunnel},
   language = {eng},
   issn = {1077-2626},
   journal = {IEEE Transactions on Visualization and Computer Graphics},
   title = {AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics},
   volume = {22},
   year = {2016}
}

TY  - JOUR
ID  - 1309622
AU  - Byška, Jan - Muzic, Mathieu Le - Gröller, Eduard - Viola, Ivan - Kozlíková, Barbora
PY  - 2016
TI  - AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
JF  - IEEE Transactions on Visualization and Computer Graphics
VL  - 22
IS  - 1
SP  - 747-756
EP  - 747-756
PB  - IEEE
SN  - 10772626
KW  - protein;aggregation;interaction;molecular dynamics;tunnel
N2  - 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.
ER  -

BYŠKA, Jan; Mathieu Le MUZIC; Eduard GRÖLLER; Ivan VIOLA a Barbora KOZLÍKOVÁ. AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. \textit{IEEE Transactions on Visualization and Computer Graphics}. IEEE, 2016, roč.~22, č.~1, s.~747-756. ISSN~1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2015.2467434.

Přehled o publikaci