Unfolding and Interactive Exploration of Protein Tunnels and
their Dynamics.

D 2016

Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics.

KOLESÁR, Ivan; Jan BYŠKA; Julius PARULEK; Helwig HAUSER; Barbora KOZLÍKOVÁ et al.

Základní údaje

Originální název

Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics.

Autoři

KOLESÁR, Ivan; Jan BYŠKA ; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ

Vydání

Bergen, EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine, od s. nestránkováno, 10 s. 2016

Nakladatel

The Eurographics Association

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/16:00090614

Organizační jednotka

Fakulta informatiky

ISBN

978-3-03868-010-9

ISSN

DOI

https://doi.org/10.2312/vcbm.20161265

EID Scopus

2-s2.0-85085759527

Klíčová slova anglicky

protein;tunnel;unfolding;comparison

Změněno: 27. 8. 2019 12:03, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for the comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems with traditional tunnel representations while providing users a quick way to navigate through the input dataset and to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated by case studies conducted by domain experts.

Citovat

KOLESÁR, Ivan; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics. Online. In Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold. EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine. Bergen: The Eurographics Association, 2016, s. nestránkováno, 10 s. ISBN 978-3-03868-010-9. Dostupné z: https://doi.org/10.2312/vcbm.20161265.

@inproceedings{1352232,
   author = {Kolesár, Ivan and Byška, Jan and Parulek, Julius and Hauser, Helwig and Kozlíková, Barbora},
   address = {Bergen},
   booktitle = {EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine},
   doi = {https://doi.org/10.2312/vcbm.20161265},
   editor = {Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold},
   keywords = {protein;tunnel;unfolding;comparison},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Bergen},
   isbn = {978-3-03868-010-9},
   pages = {nestránkováno},
   publisher = {The Eurographics Association},
   title = {Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics.},
   year = {2016}
}

TY  - CONF
ID  - 1352232
AU  - Kolesár, Ivan - Byška, Jan - Parulek, Julius - Hauser, Helwig - Kozlíková, Barbora
PY  - 2016
TI  - Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics.
PB  - The Eurographics Association
CY  - Bergen
SN  - 9783038680109
KW  - protein;tunnel;unfolding;comparison
N2  - The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for the comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems with traditional tunnel representations while providing users a quick way to navigate through the input dataset and to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated by case studies conducted by domain experts.
ER  -

KOLESÁR, Ivan; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics. Online. In Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold. \textit{EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine}. Bergen: The Eurographics Association, 2016, s.~nestránkováno, 10 s. ISBN~978-3-03868-010-9. Dostupné z: https://doi.org/10.2312/vcbm.20161265.

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