Massimiliano Bonomi

The paper develops GPCRmd-NMR, an integrative platform combining MD simulations and NMR spectroscopy to analyze GPCR dynamics at unprecedented scale.

The paper measures electrostatic potentials of histone H3 tails using NMR and simulations to show how arginine-lysine balance affects their conformational behavior in nucleosome core particles.

Adding Boltz2 distogram edges and features to protein and RNA graph networks beats MD-correlation graphs on binding tasks and improves stability, interaction and RNA predictions without simulation.

This paper shows human glutamine synthetase forms filaments stabilized by glutamine, reducing catalytic specificity for ammonia and linking product concentration to enzyme function.

HARIBOSS++ is an updated platform for RNA-targeted drug design that includes expanded data and analysis tools for RNA-small molecule interactions.

This study uses integrative ensemble modeling to identify RNA conformations that can be targeted by small molecules, revealing ligandable sites not visible in static structures.

This paper introduces bAIes, a method that improves AlphaFold2 models using Bayesian inference to enhance virtual screening accuracy for drug discovery.

This study presents the cryo-EM structure of inactive ADGRV1 and shows it has weak constitutive activation and an alternative activation mechanism distinct from other aGPCRs.

This paper introduces bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of intrinsically disordered proteins using AlphaFold2 and molecular mechanics, showing improved accuracy over existing methods.

This study develops a method to determine accurate atomic resolution conformational ensembles of intrinsically disordered proteins by integrating MD simulations with experimental data using maximum entropy reweighting.

This study shows that acylation stabilizes the native fold of CyaA and facilitates its membrane orientation, revealing how post-translational modification drives toxin activity.

The paper refines cryo-EM RNA structures using all-atom simulations and metainference to account for structural flexibility, revealing inaccuracies in single-structure approaches.

This paper introduces EMMIVox, a Bayesian method for refining cryo-EM maps into high-quality structural models and ensembles, balancing data fit with physico-chemical accuracy.

SHAMAN identifies small-molecule binding sites in RNA conformational ensembles using molecular dynamics and enhanced-sampling techniques, successfully detecting experimentally resolved pockets in benchmark tests.

HARIBOSS is a curated database of RNA-small molecule structures to support rational drug design by providing insights into RNA-ligand interactions.

The paper introduces a Bayesian scoring function to rank structural models using cryo-EM data and other information, validated on known complexes and implemented in an open-source platform.

This paper introduces a method to simultaneously determine protein structure and dynamics from cryo-electron microscopy data, applied to the STRA6 receptor.