Publications by authors named "Valerio Rizzi"

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All you need is water: Converging ligand binding simulations with hydration collective variables.
Marc Schulze, Tetiana Khakhula, Nicola Piasentin, Simone Aureli, Valerio Rizzi

J Chem Phys· October 2025

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The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.
Valerio Rizzi, Margaux Héritier, Nicola Piasentin, Simone Aureli, Francesco Luigi Gervasio

J Phys Chem Lett· September 2025

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Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation.
Simone Aureli, Valerio Rizzi, Nicola Piasentin, Francesco Luigi Gervasio

J Chem Theory Comput· August 2025

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PLUMED Tutorials: A collaborative, community-driven learning ecosystem.
Gareth A Tribello, Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Blake I Armstrong, Valerio Rizzi

J Chem Phys· March 2025

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Enhanced Sampling with Suboptimal Collective Variables: Reconciling Accuracy and Convergence Speed.
Dhiman Ray, Valerio Rizzi

J Chem Theory Comput· January 2025

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Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.
Simone Aureli, Francesco Bellina, Valerio Rizzi, Francesco Luigi Gervasio

J Chem Inf Model· November 2024

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Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.
Pedro Febrer Martinez, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio

J Chem Theory Comput· November 2024

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Absolute Binding Free Energies with OneOPES.
Maurice Karrenbrock, Alberto Borsatto, Valerio Rizzi, Dominykas Lukauskis, Simone Aureli

J Phys Chem Lett· October 2024

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DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables.
Thorben Fröhlking, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio

J Chem Phys· September 2024

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Deep learning path-like collective variable for enhanced sampling molecular dynamics.
Thorben Fröhlking, Luigi Bonati, Valerio Rizzi, Francesco Luigi Gervasio

J Chem Phys· May 2024

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SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein-Protein Interfaces.
Alberto Borsatto, Eleonora Gianquinto, Valerio Rizzi, Francesco Luigi Gervasio

J Chem Theory Comput· April 2024

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Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Valerio Rizzi

J Chem Inf Model· February 2024

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Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.
Maurice Karrenbrock, Valerio Rizzi, Piero Procacci, Francesco Luigi Gervasio

J Phys Chem B· February 2024

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Cation Chloride Cotransporter NKCC1 Operates through a Rocking-Bundle Mechanism.
Manuel José Ruiz Munevar, Valerio Rizzi, Corinne Portioli, Pietro Vidossich, Erhu Cao

J Am Chem Soc· January 2024

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OneOPES, a Combined Enhanced Sampling Method to Rule Them All.
Valerio Rizzi, Simone Aureli, Narjes Ansari, Francesco Luigi Gervasio

J Chem Theory Comput· September 2023

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Rare Event Kinetics from Adaptive Bias Enhanced Sampling.
Dhiman Ray, Narjes Ansari, Valerio Rizzi, Michele Invernizzi, Michele Parrinello

J Chem Theory Comput· November 2022

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Water regulates the residence time of Benzamidine in Trypsin.
Narjes Ansari, Valerio Rizzi, Michele Parrinello

Nat Commun· September 2022

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Discover, Sample, and Refine: Exploring Chemistry with Enhanced Sampling Techniques.
Umberto Raucci, Valerio Rizzi, Michele Parrinello

J Phys Chem Lett· February 2022

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Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution.
Narjes Ansari, Valerio Rizzi, Paolo Carloni, Michele Parrinello

J Am Chem Soc· August 2021

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The role of water in host-guest interaction.
Valerio Rizzi, Luigi Bonati, Narjes Ansari, Michele Parrinello

Nat Commun· January 2021

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Data-Driven Collective Variables for Enhanced Sampling.
Luigi Bonati, Valerio Rizzi, Michele Parrinello

J Phys Chem Lett· April 2020

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Path integral molecular dynamics for bosons.
Barak Hirshberg, Valerio Rizzi, Michele Parrinello

Proc Natl Acad Sci U S A· October 2019

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Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis.
Valerio Rizzi, Dan Mendels, Emilia Sicilia, Michele Parrinello

J Chem Theory Comput· August 2019

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The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study.
Valerio Rizzi, Daniela Polino, Emilia Sicilia, Nino Russo, Michele Parrinello

Angew Chem Int Ed Engl· March 2019

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Inelastic electron injection in a water chain.
Valerio Rizzi, Tchavdar N Todorov, Jorge J Kohanoff

Sci Rep· March 2017

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