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arXiv · 2412.13223

Generative modeling of protein ensembles guided by crystallographic electron densities

Sai Advaith Maddipatla·Nadav Bojan Sellam·Sanketh Vedula·Ailie Marx·Alex Bronstein
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Abstract

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.

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Sai Advaith Maddipatla, Nadav Bojan Sellam, Sanketh Vedula, Ailie Marx, Alex Bronstein. 2024-12-17. Generative modeling of protein ensembles guided by crystallographic electron densities. https://arxiv.org/abs/2412.13223

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