MoleCollar and Tunnel Heat Map Visualizations for Conveying
Spatio-Temporo-Chemical Properties Across and Along Protein
Voids

J 2015

MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids

BYŠKA, Jan; Adam JURČÍK; Eduard M. GRÖLLER; Ivan VIOLA; Barbora KOZLÍKOVÁ et. al.

Základní údaje

Originální název

MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids

Autoři

BYŠKA, Jan (203 Česká republika, domácí); Adam JURČÍK (203 Česká republika, domácí); Eduard M. GRÖLLER (40 Rakousko); Ivan VIOLA (703 Slovensko) a Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí)

Vydání

Computer Graphics Forum, Wiley-Blackwell, 2015, 0167-7055

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 1.542

Kód RIV

RIV/00216224:14330/15:00083057

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1111/cgf.12612

UT WoS

000358328200003

EID Scopus

2-s2.0-84937897690

Klíčová slova anglicky

protein;tunnel;heat map;molecular dynamics

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 5. 2016 06:09, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

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; Adam JURČÍK; Eduard M. GRÖLLER; Ivan VIOLA a 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, roč. 34, č. 3, s. 1-10. ISSN 0167-7055. Dostupné z: https://dx.doi.org/10.1111/cgf.12612.

@article{1300513,
   author = {Byška, Jan and Jurčík, Adam and Gröller, Eduard M. and Viola, Ivan and Kozlíková, Barbora},
   article_number = {3},
   doi = {http://dx.doi.org/10.1111/cgf.12612},
   keywords = {protein;tunnel;heat map;molecular dynamics},
   language = {eng},
   issn = {0167-7055},
   journal = {Computer Graphics Forum},
   title = {MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids},
   volume = {34},
   year = {2015}
}

TY  - JOUR
ID  - 1300513
AU  - Byška, Jan - Jurčík, Adam - Gröller, Eduard M. - Viola, Ivan - Kozlíková, Barbora
PY  - 2015
TI  - MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
JF  - Computer Graphics Forum
VL  - 34
IS  - 3
SP  - 1-10
EP  - 1-10
PB  - Wiley-Blackwell
SN  - 01677055
KW  - protein;tunnel;heat map;molecular dynamics
N2  - 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.
ER  -

BYŠKA, Jan; Adam JURČÍK; Eduard M. GRÖLLER; Ivan VIOLA a Barbora KOZLÍKOVÁ. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2015, roč.~34, č.~3, s.~1-10. ISSN~0167-7055. Dostupné z: https://dx.doi.org/10.1111/cgf.12612.

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