Author

Tristan Bereau

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Preprint Oct 2026

Predictable Accuracy of Martini 3 Absolute Protein-Ligand Binding Free Energies across 15 Targets

Alchemical free-energy calculations predict protein-ligand binding affinities with close-to-experimental accuracy, but their cost restricts them to small sets of ligands. Coarse-grained (CG) models such as Martini 3 retain a rigorous statistical-mechanical treatment at a fraction of this cost, yet their accuracy for pr...

Luis J. Walter, Tristan Bereau · 0 citations

#machine learning Preprint Sep 2026

Recovering molecules from coarse-grained beads: free-energy-conditioned generative backmapping across chemical space

This work forms compositional backmapping as conditional graph generation by introducing juniper, a discrete denoising diffusion model over molecular graphs conditioned on the octanol--water partition free energy, the principal driver of MARTINI bead type assignment and hence a proxy for bead identity.

Luis Itza Vazquez-Salazar, Tristan Bereau · 0 citations