Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction

chen, x.; zhang, y.; lu, c.; ma, w.; guan, j.; gong, c.; yang, j.; zhang, h.; zhang, k.; wu, s.; zhou, k.; yang, y.; liu, z.; wang, l.; shi, b.; shi, s.; xiao, w.

doi:10.1101/2025.01.08.631967

bioRxiv · 10.1101/2025.01.08.631967

Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction

chen, x.·zhang, y.·lu, c.·ma, w.·guan, j.·gong, c.·yang, j.·zhang, h.·zhang, k.·wu, s.·zhou, k.·yang, y.·liu, z.·wang, l.·shi, b.·shi, s.·xiao, w.

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Abstract

In this technical report, we present Protenix, a comprehensive reproduction of AlphaFold3 (AF3), aimed at advancing the field of biomolecular structure prediction. Protenix tackles the challenges of predicting complex interactions involving proteins, ligands, and nucleic acids, while enhancing accessibility and reproducibility. Across diverse benchmarks, including PoseBusters V2, low-homology PDB sets, and CASP15 RNA, Protenix achieves state-of-the-art performance in protein-ligand, protein-protein, and protein-nucleic acid predictions. We also address limitations, such as potential memorization effects, and outline future directions for improvement. By open-sourcing Protenix, we aim to democratize advanced structure prediction tools and accelerate interdisciplinary research in computational biology and drug discovery.

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chen, x., zhang, y., lu, c., ma, w., guan, j., gong, c., yang, j., zhang, h., zhang, k., wu, s., zhou, k., yang, y., liu, z., wang, l., shi, b., shi, s., xiao, w.. 2025-01-11. Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction. https://doi.org/10.1101/2025.01.08.631967

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