Visual Analysis of Ligand Trajectories in Molecular Dynamics

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. In IEEE Pacific Visualization Symposium 2019. Bangkok, Thailand: IEEE. p. 212-221. ISBN 978-1-5386-9226-4. doi:10.1109/PacificVis.2019.00032. 2019.

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

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Thailand
• Confidentiality degree: is not subject to a state or trade secret
• 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: 2165-8765
• Doi: http://dx.doi.org/10.1109/PacificVis.2019.00032
• UT WoS: 000502097000020
• Keywords in English: trajectory;ligand;protein;molecular dynamics;visualization;visual analysis
• Tags: firank_B
• Tags: International impact, Reviewed

Abstract

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