From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology

Alireza Abbaszadeh; Armita Shahlaee

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arXiv · 2508.18446

From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology

Alireza Abbaszadeh·Armita Shahlaee

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Abstract

AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware optimization strategies. These innovations dramatically improve predictive accuracy and generalization across diverse protein families, surpassing previous methods. Crucially, AlphaFold 3 embodies a paradigm shift toward differentiable simulation, bridging traditional static structural modeling with dynamic molecular simulations. By reframing protein folding predictions as a differentiable process, AlphaFold 3 serves as a foundational framework for integrating deep learning with physics-based molecular

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Alireza Abbaszadeh, Armita Shahlaee. 2025-08-25. From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology. https://arxiv.org/abs/2508.18446

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