Flow matching and diffusion perform comparably for biomolecular structure prediction

Summary

Flow matching and diffusion perform comparably for biomolecular structure prediction (1).

Figures

Model / Domain	Prot-Prot	Lig-Prot	DNA-Prot	RNA-Prot	Intra-Prot	Complex LDDT
Protenix	0.501	0.650	0.593	0.363	0.844	0.820
PTX-Mini	0.490	0.622	0.584	0.339	0.818	0.802
PTX-Mini-Flow	0.488	0.619	0.596	0.348	0.814	0.797
PTX-Mini-ESM	0.408	0.568	0.602	0.294	0.792	0.775
PTX-Mini-ESM-Flow	0.405	0.577	0.585	0.297	0.787	0.772
Protenix-Tiny	0.428	0.594	0.567	0.338	0.798	0.783
PTX-Tiny-Flow	0.422	0.594	0.569	0.338	0.806	0.780
Ref (1)

1.

Gong C, Chen X, Zhang Y, Song Y, Zhou H, Xiao W. Protenix-Mini: Efficient Structure Predictor via Compact Architecture, Few-Step Diffusion and Switchable pLM. 2025; Available from: https://arxiv.org/abs/2507.11839