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bioRxiv · 10.64898/2026.04.27.720983

Scaling and democratising structure-based protein function prediction with metagenomic-deepFRI

Bezshapkin, V.·Schymik, F.·Kucharski, P.·Szczerbiak, P.·Wojciechowski, J. W.·SZYDLOWSKI, L. M.·Kosciolek, T.
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Abstract

High-quality protein structure models have become widely available, offering insights into protein function, yet they remain underutilized. Here, we introduce metagenomic-deepFRI, a framework incorporating structural templates into functional annotation pipelines at speeds comparable to sequence-alignment methods. Notably, structural features improved GO term prediction confidence and Information Content by up to 50%. Applied to metagenomic datasets, the framework achieves nearly 90% annotation coverage, enabling protein function inference without explicit orthology-based transfer.

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Bezshapkin, V., Schymik, F., Kucharski, P., Szczerbiak, P., Wojciechowski, J. W., SZYDLOWSKI, L. M., Kosciolek, T.. 2026-04-29. Scaling and democratising structure-based protein function prediction with metagenomic-deepFRI. https://doi.org/10.64898/2026.04.27.720983

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