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arXiv · 2601.16955

3D Molecule Generation from Rigid Motifs via SE(3) Flows

Roman Poletukhin·Marcel Kollovieh·Eike Eberhard·Stephan Günnemann
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Abstract

Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based protein structure generation, we extend these fragmentation ideas to 3D, treating general molecules as sets of rigid-body motifs. Utilising this representation, we employ SE(3)-equivariant generative modelling for de novo 3D molecule generation from rigid motifs. In our evaluations, we observe comparable or superior results to state-of-the-art across benchmarks, surpassing it in atom stability on GEOM-Drugs, while yielding a 2x to 10x reduction in generation steps and offering 3.5x compression in molecular representations compared to the standard atom-based methods.

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Roman Poletukhin, Marcel Kollovieh, Eike Eberhard, Stephan Günnemann. 2026-01-23. 3D Molecule Generation from Rigid Motifs via SE(3) Flows. https://arxiv.org/abs/2601.16955

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