2014), an intuitive and interactive multi-body protein–protein docking method oriented toward its ease of usability. In this article, we describe UDock2, the new version of UDock ( Levieux et al. 2020) for the popularization of such methods, combining performance, user-oriented features, and comprehensive feedback for interactive manipulation is still a complicated task. Even though several works presented alternative approaches ( Lu et al. Different interactive docking methods have been released over time that notably suffers from limited usability and/or dependency on proprietary or expensive hardware ( Daunay et al. The manipulation and visualization of molecular bodies through an ergonomic and intuitive user interface in docking software still represent a challenge. By providing insight into the spatial arrangement of proteins and their binding sites, protein–protein docking simulations offer a valuable tool for understanding the mechanisms underlying complex biological processes. Such simulations have been shown to be effective in ranking the predicted geometries based on their binding energy, calculated using a molecular mechanics force-field ( Meng et al. To explore the geometry of these interactions, researchers have utilized protein–protein docking simulations, which aim to predict the relative position of the involved proteins. The critical involvement of protein–protein interactions in essential biological processes, including immunity and inflammation, has been well-established ( Braun and Gingras 2012).
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