Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes

Abstract

Fig. 1. Exploration of an ensemble of 500 possible human nucleosome configurations, based on the following components: a) Overview Graph with main application controls; b) 3D View, showing the exploded Complex Configuration, amino acids from contact interfaces are colored according to the frequency of their interactions; c) Property View, showing properties of all Complex Configurations; d) Protein View with range filter panel; e) Residue Matrix, which also can be switched to Contact Zone List View, and f) Filter View.Abstract-When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the datafrom the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

“…Such techniques can allow users to reveal different levels of detail on‐demand [AKCL19], incorporate focus+context techniques, as in the CLISD view of protein‐ligand interactions by Schatz et al [SFS*21], allow filtering of subsets of trajectories [JFB*19], and allow users to jump to different parts of the simulation timeline [DHR*18]. Visual abstraction of the hierarchical structure of molecules may also be exploited for the analysis of different configurations of protein complexes [FJK*19]. Many works visualize 3D molecular structures alongside interaction energies and other important molecular parameters.…”