Tag: Protein AI
Protein language models, AlphaFold, ESM3, RFDiffusion, structure prediction, protein design AI
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RFdiffusion and ProteinMPNN: How AI Now Designs Proteins From Scratch
RFdiffusion generates protein backbones. ProteinMPNN designs the sequences that fold into them. Together they achieved sub-Angstrom accuracy at influenza binding interfaces. How the two-step pipeline works, why AI-generative…
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ESM3: The Protein Language Model That Unifies Sequence, Structure and Function
ESM3 from EvolutionaryScale is a 98B-parameter generative protein language model that reasons across sequence, structure, and function simultaneously. How the VQ-VAE structural tokenization works, what the GFP design…
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AlphaFold 3 in Drug Discovery: Where It Works and Where It Fails
AlphaFold 3 predicts protein backbones well but fails significantly on ligand-binding poses in GPCR drug targets, which represent 33% of approved drugs. Five PubMed-sourced studies covering what works,…
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AlphaFold 3: What It Gets Right and Where It Still Fails
AlphaFold 3 improves GPCR backbone prediction over AF2 but shows significant discrepancies in ligand-binding poses for ions, peptides, and protein ligands. PubMed-sourced evidence from the Shanghai Institute of…
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How Protein Language Models Learned to Design Dangerous Proteins
Researchers used three open-source protein design models to bypass DNA synthesis screening in 2025. Here is how protein language models work, why training data exclusion fails as a…
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