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bioRxiv · 10.1101/2025.01.31.634501

MeTrEx: Membrane Trajectory Explorer

Jaeger-Honz, S.·Rohse, C.·Ehrmann, B.·Klein, K.·Zhang, Y.·Ma, W.·Hamada, Y.·Li, J.·Schreiber, F.
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Abstract

BackgroundMolecular Dynamics (MD) simulations provide valuable insights into the behaviour of biomolecules, particularly in complex systems such as cellular membranes. However, the increasing volume of MD data presents significant challenges in data visualisation, exploration and analysis. ResultWe present MeTrEx (Membrane Trajectory Explorer), a Python-based software designed to enhance the exploration and analysis of MD simulation data, with a focus on ligand and membrane molecule interactions. MeTrEx offers an intuitive graphical user interface for visualisation, advanced interaction tools, and comprehensive analytical capabilities. The software also supports comparative analyses of molecular trajectories and integrates external datasets for a more holistic view. A case study analysing the interaction of Polymyxin B1 with a bacterial membrane demonstrates the tools capabilities to investigate complex molecular behaviours. ConclusionBy combining detailed molecular analysis with interactive visualisation, MeTrEx provides researchers with a powerful platform to investigate complex biomolecular systems, contributing to a deeper understanding of ligand-membrane interactions.

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Jaeger-Honz, S., Rohse, C., Ehrmann, B., Klein, K., Zhang, Y., Ma, W., Hamada, Y., Li, J., Schreiber, F.. 2025-02-05. MeTrEx: Membrane Trajectory Explorer. https://doi.org/10.1101/2025.01.31.634501

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