Visual Analysis of Ligand Trajectories in Molecular Dynamics

D 2019

Visual Analysis of Ligand Trajectories in Molecular Dynamics

JURČÍK, Adam, Katarína FURMANOVÁ, Jan BYŠKA, Vojtěch VONÁSEK, Ondřej VÁVRA et. al.

Basic information

Original name

Visual Analysis of Ligand Trajectories in Molecular Dynamics

Authors

JURČÍK, Adam (203 Czech Republic, belonging to the institution), Katarína FURMANOVÁ (703 Slovakia, belonging to the institution), Jan BYŠKA (203 Czech Republic, belonging to the institution), Vojtěch VONÁSEK (203 Czech Republic), Ondřej VÁVRA (203 Czech Republic, belonging to the institution), Pavol ULBRICH (703 Slovakia, belonging to the institution), Helwig HAUSER and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Bangkok, Thailand, IEEE Pacific Visualization Symposium 2019, p. 212-221, 10 pp. 2019

Publisher

IEEE

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Thailand

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

RIV identification code

RIV/00216224:14330/19:00107231

Organization unit

Faculty of Informatics

ISBN

978-1-5386-9226-4

ISSN

DOI

http://dx.doi.org/10.1109/PacificVis.2019.00032

UT WoS

000502097000020

Keywords in English

trajectory;ligand;protein;molecular dynamics;visualization;visual analysis

Abstract

V originále

In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. These trajectories are predicted with in-silico methods that produce large ensembles of possible trajectories. In this paper, we propose a novel approach to the interactive visual exploration and analysis of large sets of ligand trajectories, enabling the domain experts to understand protein function based on the trajectory properties. The proposed solution is composed of multiple linked 2D and 3D views, enabling the interactive exploration and filtering of trajectories in an informed way. In the workflow, we focus on the practical aspects of the interactive visual analysis specific to ligand trajectories. We adapt the small multiples principle to resolve an overly large number of trajectories into smaller chunks that are easier to analyze. We describe how drill-down techniques can be used to create and store selections of the trajectories with desired properties, enabling the comparison of multiple datasets. In appropriately designed 2D and 3D views, biochemists can either observe individual trajectories or choose to aggregate the information into a functional boxplot or density visualization. Our solution is based on a tight collaboration with the domain experts, aiming to address their needs as much as possible. The usefulness of our novel approach is demonstrated by two case studies, conducted by the collaborating protein engineers.

Links

GA17-07690S, research and development project

Name: Metody identifikace a vizualizace tunelů pro flexibilní ligandy v dynamických proteinech (Acronym: FLigComp)

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

Citovat

JURČÍK, Adam, Katarína FURMANOVÁ, Jan BYŠKA, Vojtěch VONÁSEK, Ondřej VÁVRA, Pavol ULBRICH, Helwig HAUSER and Barbora KOZLÍKOVÁ. Visual Analysis of Ligand Trajectories in Molecular Dynamics. Online. In IEEE Pacific Visualization Symposium 2019. Bangkok, Thailand: IEEE, 2019, p. 212-221. ISBN 978-1-5386-9226-4. Available from: https://dx.doi.org/10.1109/PacificVis.2019.00032.

@inproceedings{1486438,
   author = {Jurčík, Adam and Furmanová, Katarína and Byška, Jan and Vonásek, Vojtěch and Vávra, Ondřej and Ulbrich, Pavol and Hauser, Helwig and Kozlíková, Barbora},
   address = {Bangkok, Thailand},
   booktitle = {IEEE Pacific Visualization Symposium 2019},
   doi = {http://dx.doi.org/10.1109/PacificVis.2019.00032},
   keywords = {trajectory;ligand;protein;molecular dynamics;visualization;visual analysis},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Bangkok, Thailand},
   isbn = {978-1-5386-9226-4},
   pages = {212-221},
   publisher = {IEEE},
   title = {Visual Analysis of Ligand Trajectories in Molecular Dynamics},
   year = {2019}
}

TY  - JOUR
ID  - 1486438
AU  - Jurčík, Adam - Furmanová, Katarína - Byška, Jan - Vonásek, Vojtěch - Vávra, Ondřej - Ulbrich, Pavol - Hauser, Helwig - Kozlíková, Barbora
PY  - 2019
TI  - Visual Analysis of Ligand Trajectories in Molecular Dynamics
PB  - IEEE
CY  - Bangkok, Thailand
SN  - 9781538692264
KW  - trajectory;ligand;protein;molecular dynamics;visualization;visual analysis
N2  - In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. These trajectories are predicted with in-silico methods that produce large ensembles of possible trajectories. In this paper, we propose a novel approach to the interactive visual exploration and analysis of large sets of ligand trajectories, enabling the domain experts to understand protein function based on the trajectory properties. The proposed solution is composed of multiple linked 2D and 3D views, enabling the interactive exploration and filtering of trajectories in an informed way. In the workflow, we focus on the practical aspects of the interactive visual analysis specific to ligand trajectories. We adapt the small multiples principle to resolve an overly large number of trajectories into smaller chunks that are easier to analyze. We describe how drill-down techniques can be used to create and store selections of the trajectories with desired properties, enabling the comparison of multiple datasets. In appropriately designed 2D and 3D views, biochemists can either observe individual trajectories or choose to aggregate the information into a functional boxplot or density visualization. Our solution is based on a tight collaboration with the domain experts, aiming to address their needs as much as possible. The usefulness of our novel approach is demonstrated by two case studies, conducted by the collaborating protein engineers.
ER  -

JURČÍK, Adam, Katarína FURMANOVÁ, Jan BYŠKA, Vojtěch VONÁSEK, Ondřej VÁVRA, Pavol ULBRICH, Helwig HAUSER and Barbora KOZLÍKOVÁ. Visual Analysis of Ligand Trajectories in Molecular Dynamics. Online. In \textit{IEEE Pacific Visualization Symposium 2019}. Bangkok, Thailand: IEEE, 2019, p.~212-221. ISBN~978-1-5386-9226-4. Available from: https://dx.doi.org/10.1109/PacificVis.2019.00032.

Detailed Information on Publication Record