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Volume 6 Issue 6, June 2026

Structure-aware de novo ligand generation

Although several methods have been developed for ligand generation, many suffer from prolonged sampling times or struggle to produce realistic structures. In this issue, Julian Cremer et al. introduce FLOWR, a flow-matching model for de novo generation of three-dimensional ligands that improves upon existing approaches in both generative quality and computational efficiency. In addition, the authors establish FLOWR.MULTI, an interaction- and fragment-conditional design tool that does not require retraining or resampling strategies. Finally, they address ongoing data leakage issues and pose quality concerns with SPINDR, a benchmark dataset for structure-based drug design.

See Cremer et al.

Image: Konstantin Shaklein / Alamy. Cover design: Alex Wing

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Research Briefings

  • We developed FLOWR, a structure-aware multi-purpose generative model unifying de novo ligand generation, fragment-based and interaction-conditional sampling. We demonstrated that FLOWR generates ligands up to 70-fold faster compared with existing methods while improving the physical validity and interaction accuracy of generated compounds.

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