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On Diffusion Posterior Sampling via Sequential Monte Carlo for Zero-Shot Scaffolding of Protein Motifs

8 Dec 2024arXiv:2412.05788archive 2025-07-28

James Matthew Young, O. Deniz Akyildiz

With the advent of diffusion models, new proteins can be generated at an unprecedented rate. The \textit{motif scaffolding problem} requires steering this generative process to yield proteins with a desirable functional substructure -- a motif. While models have been trained to take the motif as conditional input, recent techniques in diffusion posterior sampling can be leveraged as zero-shot alternatives whose approximations can be corrected with sequential Monte Carlo (SMC) algorithms. In this work, we introduce a new set of guidance potentials to describe and solve scaffolding tasks by adapting SMC-aided diffusion posterior samplers with an unconditional model, Genie, acting as a prior. Against established benchmarks, we successfully scaffold several single-motif and multi-motif problems. The latter is possible by pairing reconstruction guidance with SE(3)-invariant potentials. In the single-motif case, we find these potentials perform comparably to the conventional masking approach and that reconstruction guidance outperforms replacement methods when aided with SMC. We additionally consider a guidance potential for point symmetry constraints and produce designable internally symmetric monomers with our setup. Overall, this work highlights the capabilities and areas for improvement of zero-shot posterior samplers in motif scaffolding tasks. Code is available at: https://github.com/matsagad/mres-project

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