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.

Základní údaje

Originální název

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

Autoři

FURMANOVÁ, Katarína (703 Slovensko, domácí), Adam JURČÍK (203 Česká republika, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí), Helwig HAUSER a Jan BYŠKA (203 Česká republika, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Kanada

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.579

Kód RIV

RIV/00216224:14330/20:00113971

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1109/TVCG.2019.2934333

UT WoS

000506166100078

Klíčová slova anglicky

Molecular Visualization; Data Filtering; Coordinated and Multiple Views

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 4. 2021 07:54, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

GC18-18647J, projekt VaV

Název: Vizuální analýza interakcí proteinů a ligandů (Akronym: PROLINT)

Investor: Grantová agentura ČR, Visual Analysis of Protein-Ligand Interactions

MUNI/A/1040/2018, interní kód MU

Název: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 19 (Akronym: SKOMU)

Investor: Masarykova univerzita, Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 19, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

MUNI/M/0822/2015, interní kód MU

Název: Expressive Visualization of Protein Complexes

Investor: Masarykova univerzita, Expressive Visualization of Protein Complexes, INTERDISCIPLINARY - Mezioborové výzkumné projekty

Citovat

FURMANOVÁ, Katarína, Adam JURČÍK, Barbora KOZLÍKOVÁ, Helwig HAUSER a 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, roč. 26, č. 1, s. 843-852. ISSN 1077-2626. Dostupné z: https://dx.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 = {http://dx.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 a 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, roč.~26, č.~1, s.~843-852. ISSN~1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2019.2934333.

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