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Updated: Dec 30, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
Published on: July 19, 2024
A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes
Mauricio G S Costa1,2,3, Charline Fagnen2,3, Catherine Vénien-Bryan2
1Fundacao Oswaldo Cruz, Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900 Rio de Janeiro, Brazil.
Abstract:
Previous studies demonstrated the efficiency of the Molecular Dynamics with excited Normal Modes (MDeNM) method on the characterization of large structural changes at a low computational cost. We present here MDeNM-EMfit, an extension of the original method designed to the flexible fit of structures into cryo-EM maps. Here, instead of a uniform exploration of the collective motions described by normal modes, sampling is directed toward conformations with increased correlations with the experimental map. Future perspectives to improve the accuracy of fitting and speed of calculations are discussed in light of the results.
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