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International Journal of Biological Macromolecules|January 29, 2024
Molecular dynamics simulations reveal the parallel stranded d(GGGA)<sub>3</sub>GGG DNA quadruplex folds via multiple paths from a coil-like ensemblePavlína Pokorná, Vojtěch Mlýnský, Giovanni Bussi, et al.NAR Genomics and Bioinformatics|February 12, 2021
Machine learning a model for RNA structure predictionNicola Calonaci, Alisha Jones, Francesca Cuturello, et al.Journal of the American Chemical Society|May 14, 2010
Single-molecule pulling simulations can discern active from inactive enzyme inhibitorsFrancesco Colizzi, Remo Perozzo, Leonardo Scapozza, et al.The Journal of Physical Chemistry. B|February 24, 2026
Making PLUMED Fly: A Tutorial on Optimizing PerformanceDaniele Rapetti, Massimiliano Bonomi, Carlo Camilloni, et al.RNA (New York, N.Y.)|November 14, 2018
Barnaba: software for analysis of nucleic acid structures and trajectoriesSandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, et al.Journal of Chemical Theory and Computation|February 28, 2023
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy CalculationsWei-Tse Hsu, Valerio Piomponi, Pascal T Merz, et al.Journal of Chemical Theory and Computation|November 16, 2018
Determination of Structural Ensembles of Proteins: Restraining vs ReweightingRamya Rangan, Massimiliano Bonomi, Gabriella T Heller, et al.Journal of Chemical Information and Modeling|March 25, 2026
Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and ChallengesZhengyue Zhang, Gaia Dolcetti, Christian Tyrchan, et al.Science Advances|May 26, 2018
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulationsSandro Bottaro, Giovanni Bussi, Scott D Kennedy, et al.Journal of Chemical Theory and Computation|May 4, 2019
Fitting Corrections to an RNA Force Field Using Experimental DataAndrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, et al.Pageof 12