Nadav Bojan Sellam

Sai Advaith Maddipatla, Nadav Bojan Sellam, Sanketh Vedula et al.

Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein structures to these measurements is a challenging, ill-posed inverse problem. We propose a non-i.i.d. ensemble guidance approach to solve this problem using existing protein structure generative models and demonstrate that it accurately recovers complicated multi-modal alternate protein backbone conformations observed in certain single crystal measurements.

Nadav Bojan Sellam, Meital Bojan, Paul Schanda et al.

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.