Author

Filipe Menezes

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Open access Sep 2026

Local structural preference maps encode transferable protein-interface energetics

Relating the drivers of binding affinity to structural features remains difficult because affinity emerges from many weak, context-dependent interactions, while experimental affinity and mutation data are limited. Here, we ask whether a machine-learning model can learn energetically relevant interaction preferences dir...

Maximilian Kienlein, Filipe Menezes, Phillip Grass et al. · bioRxiv · 0 citations

Oct 2025

Flowr.root – A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction

Flowr.root achieves state-of-the-art performance in both unconditional 3D molecule and pocket-conditional ligand generation, producing geometrically realistic, low-strain structures with computational efficiency on established benchmark datasets.

Julian Cremer, Tuan Le, M. Ghahremanpour et al. · arXiv.org · 5 citations · ⚡1