Publications by authors named "Valerio Piomponi"

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Evolutionary Constraints Guide AlphaFold2 in Predicting Alternative Conformations and Inform Rational Mutation Design.
Valerio Piomponi, Alberto Cazzaniga, Francesca Cuturello

J Chem Inf Model· September 2025

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Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.
Christoph Müller-Hermes, Valerio Piomponi, Stefan Hilber, Sam Asami, Christoph Kreutz

Nucleic Acids Res· June 2025

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MDRefine: A Python package for refining molecular dynamics trajectories with experimental data.
Ivan Gilardoni, Valerio Piomponi, Thorben Fröhlking, Giovanni Bussi

J Chem Phys· May 2025

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Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction.
Valerio Piomponi, Miroslav Krepl, Jiri Sponer, Giovanni Bussi

J Phys Chem B· September 2024

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Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations.
Wei-Tse Hsu, Valerio Piomponi, Pascal T Merz, Giovanni Bussi, Michael R Shirts

J Chem Theory Comput· March 2023

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Molecular Simulations Matching Denaturation Experiments for N-Methyladenosine.
Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi

ACS Cent Sci· August 2022

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