Author

Laura Orellana

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Open access Sep 2026

Leveraging elastic networks in a coarse-grained brownian simulation framework for protein conformational dynamics

Protein dynamics is fundamental to understand mechanisms. Although atomistic Molecular Dynamics (MD) remains the gold standard for predicting protein motions, its computational cost limits applications at large scales. Here, we present a coarse-grained (CG) simulation framework that combines Elastic Network Models (ENM...

Domenico Scaramozzino, Enrica Ruggeri, Mariia Feshyna et al. · bioRxiv · 0 citations

#protein folding Open access Aug 2026

Modeling conformational transitions in DNA, RNA, and protein–nucleic acid complexes

A generalized essential dynamics-refined ENM (edENM) is introduced for both DNA, RNA, and protein-nucleic acid complexes, parametrized against a diverse set of molecular dynamics simulations and validated using experimental ensembles from nuclear magnetic resonance, X-ray crystallography, and cryogenic electron microsc...

Domenico Scaramozzino, Marco Cannariato, Byung Ho Lee et al. · Nucleic Acids Research · 1 citation