Dy-Bendix: Visual Analysis approach of α helices molecular dynamics simulations
Abstract
α helices are one of the most common folding patterns found in proteins. They are of great importance in the context of molecular dynamics simulations, as they contribute to structural stability, conformational dynamics and molecular interactions, providing crucial information on protein behavior and function at the atomic scale. Here is presented Dy-Bendix (Dynamic Bendix), a novel representation of helices dynamics based on an intuitive helix geometry abstraction named Bendix. Indeed, in this work, we considered α helices fluctuation to quantify and represent the movement amplitude of α helices during the molecular dynamics. To do so, we used UnityMol, an open source molecular viewer and prototyping platform. We looked at the amplitude of movement of the residues that make up the helix during a simulation. These movement amplitudes are represented by a coloured heat map on the Bendix surface. This representation allows to detect instinctively helices with big movements and facilitate the comparison of helices movement using the heat-map color throughout the trajectory visualization. It also allows the visualization of the molecular dynamics in static image.
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