Multiscale Visual Drilldown for the Analysis of Large Ensembles
of Multi-Body Protein Complexes

J 2020

Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes

FURMANOVÁ, Katarína; Adam JURČÍK; Barbora KOZLÍKOVÁ; Helwig HAUSER; Jan BYŠKA et. al.

Basic information

Original name

Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes

Authors

FURMANOVÁ, Katarína (703 Slovakia, belonging to the institution); Adam JURČÍK (203 Czech Republic, belonging to the institution); Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution); Helwig HAUSER and Jan BYŠKA (203 Czech Republic, belonging to the institution)

Edition

IEEE Transactions on Visualization and Computer Graphics, IEEE, 2020, 1077-2626

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Canada

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 4.579

RIV identification code

RIV/00216224:14330/20:00113971

Organization unit

Faculty of Informatics

DOI

https://doi.org/10.1109/TVCG.2019.2934333

UT WoS

000506166100078

EID Scopus

2-s2.0-85075751962

Keywords in English

Molecular Visualization; Data Filtering; Coordinated and Multiple Views

Abstract

In the original language

When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data – from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.

Links

GC18-18647J, research and development project

Name: Vizuální analýza interakcí proteinů a ligandů (Acronym: PROLINT)

Investor: Czech Science Foundation

MUNI/A/1040/2018, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 19 (Acronym: SKOMU)

Investor: Masaryk University, Category A

MUNI/M/0822/2015, interní kód MU

Name: Expressive Visualization of Protein Complexes

Investor: Masaryk University, INTERDISCIPLINARY - Interdisciplinary research projects

Cite

FURMANOVÁ, Katarína; Adam JURČÍK; Barbora KOZLÍKOVÁ; Helwig HAUSER and Jan BYŠKA. Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020, vol. 26, No 1, p. 843-852. ISSN 1077-2626. Available from: https://doi.org/10.1109/TVCG.2019.2934333.

@article{1546968,
   author = {Furmanová, Katarína and Jurčík, Adam and Kozlíková, Barbora and Hauser, Helwig and Byška, Jan},
   article_number = {1},
   doi = {https://doi.org/10.1109/TVCG.2019.2934333},
   keywords = {Molecular Visualization; Data Filtering; Coordinated and Multiple Views},
   language = {eng},
   issn = {1077-2626},
   journal = {IEEE Transactions on Visualization and Computer Graphics},
   title = {Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes},
   url = {http://dx.doi.org/10.1109/TVCG.2019.2934333},
   volume = {26},
   year = {2020}
}

TY  - JOUR
ID  - 1546968
AU  - Furmanová, Katarína - Jurčík, Adam - Kozlíková, Barbora - Hauser, Helwig - Byška, Jan
PY  - 2020
TI  - Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes
JF  - IEEE Transactions on Visualization and Computer Graphics
VL  - 26
IS  - 1
SP  - 843-852
EP  - 843-852
PB  - IEEE
SN  - 10772626
KW  - Molecular Visualization
KW  - Data Filtering
KW  - Coordinated and Multiple Views
UR  - http://dx.doi.org/10.1109/TVCG.2019.2934333
L2  - http://dx.doi.org/10.1109/TVCG.2019.2934333
N2  - When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data – from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.
ER  -

FURMANOVÁ, Katarína; Adam JURČÍK; Barbora KOZLÍKOVÁ; Helwig HAUSER and Jan BYŠKA. Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes. \textit{IEEE Transactions on Visualization and Computer Graphics}. IEEE, 2020, vol.~26, No~1, p.~843-852. ISSN~1077-2626. Available from: https://doi.org/10.1109/TVCG.2019.2934333.

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