Publications by authors named "Simone Aureli"

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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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Learning committor-consistent collective variables.
Thorben Fröhlking, Simone Aureli, Francesco Luigi Gervasio

Nat Comput Sci· July 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, Simone Aureli

J Chem Phys· March 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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Structural basis of connexin-36 gap junction channel inhibition.
Xinyue Ding, Simone Aureli, Anand Vaithia, Pia Lavriha, Dina Schuster

Cell Discov· June 2024

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Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase.
Simone Aureli, Vince Bart Cardenas, Stefano Raniolo, Vittorio Limongelli

Commun Chem· November 2023

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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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Subcellular location defines GPCR signal transduction.
Arthur Radoux-Mergault, Lucie Oberhauser, Simone Aureli, Francesco Luigi Gervasio, Miriam Stoeber

Sci Adv· April 2023

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Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses.
Dominykas Lukauskis, Marley L Samways, Simone Aureli, Benjamin P Cossins, Richard D Taylor

J Chem Inf Model· December 2022

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Phosphorylation of FAM134C by CK2 controls starvation-induced ER-phagy.
Giorgia Di Lorenzo, Francescopaolo Iavarone, Marianna Maddaluno, Ana Belén Plata-Gómez, Simone Aureli

Sci Adv· September 2022

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Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach.
Alessandra de Felice, Simone Aureli, Vittorio Limongelli

Front Mol Biosci· May 2021

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DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis.
Simone Aureli, Daniele Di Marino, Stefano Raniolo, Vittorio Limongelli

Bioinformatics· December 2019

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How many antimicrobial peptide molecules kill a bacterium? The case of PMAP-23.
Daniela Roversi, Vincenzo Luca, Simone Aureli, Yoonkyung Park, Maria Luisa Mangoni

ACS Chem Biol· September 2014

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