Abstract
AbstractWhen studying protein‐ligand interactions, many different factors can influence the behaviour of the protein as well as the ligands. Molecular visualisation tools typically concentrate on the movement of single ligand molecules; however, viewing only one molecule can merely provide a hint of the overall behaviour of the system. To tackle this issue, we do not focus on the visualisation of the local actions of individual ligand molecules but on the influence of a protein and their overall movement. Since the simulations required to study these problems can have millions of time steps, our presented system decouples visualisation and data preprocessing: our preprocessing pipeline aggregates the movement of ligand molecules relative to a receptor protein. For data analysis, we present a web‐based visualisation application that combines multiple linked 2D and 3D views that display the previously calculated data The central view, a novel enhanced sequence diagram that shows the calculated values, is linked to a traditional surface visualisation of the protein. This results in an interactive visualisation that is independent of the size of the underlying data, since the memory footprint of the aggregated data for visualisation is constant and very low, even if the raw input consisted of several terabytes.
Highlights
IntroductionDifferent techniques and approaches have been developed so far for understanding the complex and specific interactions between ligand molecules and protein surfaces
Protein-ligand interactions are a vast and diverse field
Our project partners appreciated this, as the actual simulation, in comparison, took several days. As their goal was to study general ligand pathways, the precalculated landing spot values were of immense importance to them as they provide hints where the ligand molecules come in contact first
Summary
Different techniques and approaches have been developed so far for understanding the complex and specific interactions between ligand molecules and protein surfaces. While existing approaches for the visualisation of protein-ligand interactions, like the one by Vázquez et al [VHG*18], typically concentrate on single ligand molecules, global approaches to analyse ligand movement are rare. Streaming approaches typically use animation and are often preferred by domain scientists as they are easy to understand. Systems that use aggregated data keep track of a limited number of represented parameters. They do not calculate information such as contact counts, that are highly relevant for our collaborators
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