DockVis: Visual Analysis of Molecular Docking Trajectories

Abstract

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein–ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way, we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow‐up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (http://www.caver.cz).

From complex data to clear insights: visualizing molecular dynamics trajectories

“…The tool includes a graphical analysis feature with statistical reports on the frequency and distribution of each type of atom and interaction. Additionally, ( Furmanová et al, 2020 ), introduce DockVis as a visual analysis tool designed to work with multivariate output data from CaverDock ( Filipovič et al, 2019 ). DockVis provides interconnected 2D and 3D views, allowing to comprehend the spatial configurations of ligands as they traverse protein tunnels.…”

Survey on Visualization of Biomacromolecule

“…Byška 等 [48] 提出了基于 Focus+Context 的交 互式视觉分析方法, 用于长时间和密集的分子动 力学模拟分析. Furmanová 等 [49] 提出了分子对接轨 迹的可视化分析工具 DockVis, 使用分子对接工具 CaverDock [50] 的输出数据, 将配体及周围环境用 二三维结合的形式描述. 用户利用该工具能快速 感知蛋白质隧道中配体的空间构象, 并与视图交 互开展信息钻取.…”

Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures

“…Passage of substrates, intermediates, and products via molecular channels reduces the transit time to or from the active centers and facilitates an efficient transference within multifunctional enzymes or enzymatic complexes. Ligand transport, molecular docking trajectories, and the potential of molecular tunnels and channels in biotechnology have been recently analyzed [ 10 , 11 ]. Holding substrates in protein empty spaces can ensure substrate availability and loss of reaction intermediates by diffusion, thus increasing reaction efficiency.…”

“…A simple strategy to allow the growth of thermophiles maintaining the thermal stability of labile biomolecules was recently proposed by Cuecas et al [ 12 ]. These authors concluded that maintaining intracellular viscosity can provide thermal stability to some low-molecular-weight biomolecules although this mechanism appeared to be inefficient above 80 °C [ 10 ]. Thus, hyperthermophiles might require additional adaptations and some complementary alternatives have been proposed [ 12 , 16 , 17 ].…”