paper
arXiv cs.LG
November 18th, 2025 at 5:00 AM

Seek and You Shall Fold

arXiv:2511.13244v1 Announce Type: new Abstract: Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are non-differentiable, making them incompatible with gradient-based conditional sampling. This is especially limiting in nuclear magnetic resonance, where rich data such as chemical shifts are hard to directly integrate into generative modeling. We introduce a framework for non-differentiable guidance of protein generative models, coupling a continuous diffusion-based generator with any black-box objective via a tailored genetic algorithm. We demonstrate its effectiveness across three modalities: pairwise distance constraints, nuclear Overhauser effect restraints, and for the first time chemical shifts. These results establish chemical shift guided structure generation as feasible, expose key weaknesses in current predictors, and showcase a general strategy for incorporating diverse experimental signals. Our work points toward automated, data-conditioned protein modeling beyond the limits of differentiability.

#ai

Score: 2.80

Engagement proxy: 0

Canonical link: https://arxiv.org/abs/2511.13244