Visualization of Large Molecular Trajectories

Abstract

The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.

DockVis: Visual Analysis of Molecular Docking Trajectories

“…Duran et al . [DHR*19] presented another tool for interactive analysis of ligand trajectories, combining the 3D view with 2D plots of several properties (both geometric and chemical). Their tool focuses on suggesting the potentially interesting parts of the MD simulation to the user by highlighting the background of the graphs.…”

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization

“…Although the technique comprehensibly conveys several properties of the interaction, it is not suitable for the large trajectories and more ligands within one simulation. These limitations are addressed by Duran et al [DHR*19] who designed a tool for visual exploration of more ligands at once. Each ligand trajectory is represented by one 2D plot, showing the information about the ligand speed, distance to the active site, and energies.…”

“…There are solutions that already address some of these requirements. For instance, Duran et al [DHR*19] link 3D animations of protein‐ligand interactions with 2D plots of associated MD simulation measurements (R1). However, the 3D animation is not adapted to the exploration focus (R3, R4) and therefore hard to comprehend for long and crowded simulations.…”

Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics

“…A visual analytics tool for long molecular dynamics simulation data, described by Duran et al [15], provides an importance-driven time series analysis of integral measures of particle simulation data. They rely on time series aggregation and interval clustering based on ligand's position.…”

“…Due to the finite resolution of the display, it is impossible to show the reconstructed function for some combinations of zoom and scale. This effect is well known in the field and can be addressed for example by using a band graph [1] as in BinX [4] and Duran [15].…”