ELViM: Understanding Molecular Energy Landscape
Rafael Giordano ViegasiD, Ingrid B. S. MartinsiD, Murilo N. SanchesiD, Antonio Bento de Oliveira JunioriD, Juliana B. de CamargoiD, Fernando V. PaulovichiD, Vitor B. P. LeiteiD
Abstract
AbstractMolecular dynamics (MD) simulations provide a powerful means to explore the dynamic behavior of biomolecular systems at the atomic level. However, analyzing the vast datasets generated by MD simulations poses significant challenges. This manuscript discusses the Energy Landscape Visualization Method (ELViM), a multidimensional reduction technique inspired by energy landscape theory. ELViM transcends one-dimensional representations, offering a comprehensive analysis of the effective conformational phase space without the need for predefined reaction coordinates. We apply ELViM to study the folding landscape of the antimicrobial peptide Polybia-MP1, showcasing its versatility in capturing complex biomolecular dynamics. Using dissimilarity matrices and a force-scheme approach, ELViM provides intuitive visualizations, revealing structural correlations, and local conformational signatures. The method is demonstrated to be adaptable, robust, and applicable to various biomolecular systems.
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