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Alessia Ghidini

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Publications associées (4)

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Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein–Ligand to RNA-Ligand Binding

Andrea Cavalli, Alessia Ghidini

In this study, we addressed the challenge of estimating binding free energies in complex biological systems of pharmaceutical relevance, including both protein-ligand and RNA-ligand complexes. As case studies, we examined the intricate binding of the drug ...

American Chemical Society (ACS)2025

Bidirectional path-based non-equilibrium simulations for binding free energy

Andrea Cavalli, Alessia Ghidini

Estimating free energy is a fundamental computational challenge, especially in complex biological systems characterised by numerous degrees of freedom. In this study, we investigate the potential of leveraging non-equilibrium free energy estimators within ...

Taylor & Francis2024

Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation

Alessia Ghidini

While nowadays approaches for equilibrium free energy estimation are well established, nonequilibrium simulations represent both an appealing computational opportunity and a challenge. This kind of simulations allows for a trivially parallel scheme, but at ...

2025

Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway

Andrea Cavalli, Alessia Ghidini

American Chemical Society (ACS)2025