Interactive exploration of ligand transportation through protein tunnels

Abstract

BackgroundProtein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This prevents understanding of the ligand transportation and reasoning behind its behavior along the path.ResultsTo address the needs of the domain experts we design an explorative visualization solution based on a multi-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory by exploring different attributes of the ligand and its movement, such as its distance to the active site, changes of amino acids lining the ligand, or ligand “stuckness”. The process is supported by three linked views – 3D representation of the simplified trajectory, scatterplot matrix, and bar charts with line representation of ligand-lining amino acids.ConclusionsThe usage of our tool is demonstrated on molecular dynamics simulations provided by the domain experts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior.

Survey on Visualization of Biomacromolecule

“…Furmanová 等 [44] 通过设计概览图和条形图帮助用 户导航到配体轨迹中关注区域, 通过散点图矩阵查 看配体动态行为, 探索不同配体轨迹的特征. 此外, 通过轨迹的自动/交互式简化, 领域专家可使用三 维视图进一步探索配体轨迹空间.…”

DockVis: Visual Analysis of Molecular Docking Trajectories

“…Furmanová et al . [FJB*17] proposed a visual analysis tool for the exploration of several geometric properties of the ligand passage, such as the free space around the ligand or its speed. Additionally, they proposed methods for smoothing the originally very scattered ligand trajectory to be able to reveal trends in ligand movement.…”

Multiscale Molecular Visualization

“…They are often tailored to the exploration of specific properties, interactions, or inner cavities. The interactive exploration of a ligand trajectory inside a protein structure has been introduced by Furmanová et al [37]. The visual analysis tool consists of a multiscale simplification model of the ligand trajectory.…”