The rapid advancement of artificial intelligence (AI) is transforming the field of structural biology. In May 2024, DeepMind and Isomorphic Labs launched AlphaFold 3 (AF3), a revolutionary AI system capable of predicting the 3D structures and interactions of proteins, nucleic acids, small molecules, ions, and other biomolecules with remarkable precision.

Unlike its predecessors, AF3 uses a novel diffusion-based architecture that allows it to model complex molecular systems beyond single proteins. It achieves significantly higher accuracy in predicting protein-ligand, protein-nucleic acid, and multi-component complexes—outperforming traditional computational tools and even specialized docking software.

AF3 has already demonstrated great potential across multiple domains:

• Drug Design: It accurately predicts binding sites and interaction energies, accelerating target identification and drug optimization.
• Vaccine Development: AF3 models antigen-antibody interactions, aiding the design of more effective vaccines.
• Disease Mechanisms: Researchers use AF3 to explore protein conformational changes linked to diseases like Alzheimer’s and cancer.
• Protein Engineering: The tool supports the design of novel proteins and enzymes with tailored functions.

Despite its strengths, AF3 still faces challenges, such as predicting dynamic conformational changes and avoiding “hallucination” in disordered protein regions. However, its open-source release and ongoing improvements promise to further enhance its capabilities.

The work, titled “AlphaFold 3: an unprecedent opportunity for fundamental research and drug development,” was published in Precision Clinical Medicine on July 1, 2025.
https://doi.org/10.1093/pcmedi/pbaf015