IEEE VIS 2024 Content: InVADo: Interactive Visual Analysis of Molecular Docking Data

InVADo: Interactive Visual Analysis of Molecular Docking Data

Marco Schäfer -

Nicolas Brich -

Jan Byška -

Sérgio M. Marques -

David Bednář -

Philipp Thiel -

Barbora Kozlíková -

Michael Krone -

DOI: 10.1109/TVCG.2023.3337642

Room: Bayshore I

2024-10-16T14:39:00ZGMT-0600Change your timezone on the schedule page
2024-10-16T14:39:00Z
Exemplar figure, described by caption below
InVADo (Interactive Visual Analysis of Molecular Docking Data) is a visual analytics tool for molecular docking data. It allows users to interactively rank, filter, and cluster the docked compounds and offers a combination of linked 3D and 2D views providing information about the spatial arrangement of the molecules, the type of interaction, or propensities for certain functional groups. The goal of the exploratory visual analysis approach supported by InVADo is to support drug design and similar biochemical applications.
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Keywords

Molecular Docking, AutoDock, Virtual Screening, Visual Analysis, Visualization, Clustering, Protein-Ligand Interaction.

Abstract

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the target and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results. However, the most commonly used docking software provides no or very basic evaluation possibilities. Scripting and external molecular viewers are often used, which are not designed for an efficient analysis of docking results. Therefore, we developed InVADo, a comprehensive interactive visual analysis tool for large docking data. It consists of multiple linked 2D and 3D views. It filters and spatially clusters the data, and enriches it with post-docking analysis results of protein-ligand interactions and functional groups, to enable well-founded decision-making. In an exemplary case study, domain experts confirmed that InVADo facilitates and accelerates the analysis workflow. They rated it as a convenient, comprehensive, and feature-rich tool, especially useful for virtual screening.