M. Parrinello

Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution

The paper shows that water molecules trigger an irreversible conformational change in SARS-CoV-2 main protease when transitioning from solid to aqueous state, leading to asymmetric subunit conformations.

On the accuracy of molecular simulation-based predictions of koff values: a Metadynamics study

This paper evaluates the accuracy of molecular simulations in predicting koff values for drug unbinding using metadynamics and QM/MM methods, finding discrepancies due to force field limitations.

Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop

The paper integrates NMR and simulations to study UUCG RNA stem-loop dynamics, identifying two states and showing MD simulations overestimate a non-native conformation.

Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

The paper uses metadynamics simulations to reconstruct the full free energy landscape of neuroreceptor/ligand unbinding and identifies two escape routes for the ligand.

Accelerating the Calculation of Protein-Ligand Binding Free Energy and residence Times using Dynamically Optimized Collective Variables

This study predicts ligand binding modes and computes binding free energy and unbinding rates using a novel combination of computational methods, revealing water and solvation as dominant slow degrees of freedom.

Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables

The paper uses a variational approach to metadynamics to study conformational transitions in L99A T4 Lysozyme, identifying two intermediate states with reduced computational cost.