Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization

Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction. We present a two-stage method for ligand conformation generation guided by such templates. In the first stage, we introduce a molecular alignment approach based on flow-matching to generate 3D coordinates for the ligand, using the template structure as a reference. In the second stage, a differentiable pose optimization procedure refines this conformation based on shape and pharmacophore similarities, internal energy, and, optionally, the protein binding pocket. We evaluate our approach on a new benchmark of ligand pairs co-crystallized with the same target and show that it outperforms standard docking tools and open-access alignment methods, especially in cases involving low similarity to the template or high ligand flexibility.
View on arXiv@article{bergues2025_2506.06305, title={ Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization }, author={ Noémie Bergues and Arthur Carré and Paul Join-Lambert and Brice Hoffmann and Arnaud Blondel and Hamza Tajmouati }, journal={arXiv preprint arXiv:2506.06305}, year={ 2025 } }