Author

Domenico Scaramozzino

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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

Review Jul 2026

The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.

Addressing and predicting ligand-binding sites in protein structures, as well as the prediction of reliable structures of proteins interacting with other proteins, will be pivotal for fully details of structural mechanisms and dynamics.

Pradeep Bk, Shi-Jie Chen, R. Dima et al. · Journal of Molecular Biology · 1 citation