Protein design

Generative and modular design, from backbone diffusion to the modelling you can run on a laptop.

Other chapters

X-ray and crystallisation Cryo-EM Fundamentals Prediction and validation Protein design AI workflows and chemistry tools Docking, screening and simulation

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mdeller.com FAFFAbout ↗ forecasts where a protein is likely to stall on the road to a structure, from 335,771 real attempts in the Protein Structure Initiative arch… mdeller.com ALPHABETTI ↗ a protein sequence logo in 3D, wrapped around its own predicted structure. The amino acid letters themselves, stacked by how strongly a lang… mdeller.com ButtFold ↗ a protein folds in your browser and the trajectory becomes music: contacts forming are note onsets, hydropathy sets pitch, secondary structu… mdeller.com TopPDBLX ↗ every crystallisation condition in the protein data bank, parsed and indexed: what worked, how often, and how little of it is specific to yo… mdeller.com AlphaFraud ↗ Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures mdeller.com ChatPDB ↗ A protein-structure-literate AI assistant for analyzing proteins: RAG for facts, a QLoRA-tuned model for behaviour, and live Biopython/gemmi…

12 articles

15 Oct 2025 · 3 min read Protein Hunter: Pioneering the Next Frontier of AI-Driven Protein Design Protein Hunter: Pioneering the Next Frontier of AI-Driven Protein Design Protein Hunter: exploiting structure hallucination within diffusion for protein design Revolution… 22 Aug 2025 · 2 min read Revolutionizing Drug Discovery: LatentX and the Future of Protein Binder Design Revolutionizing Drug Discovery: LatentX and the Future of Protein Binder Design LatentX generates lab-functional protein binders with picomolar affinities and near-perfec… 14 Aug 2025 · 3 min read The New Architects: How Generative AI Is Designing Novel Protein Scaffolds The New Architects: How Generative AI Is Designing Novel Protein Scaffolds The past, present and future of de novo protein design. Nature, 2026 From renovation to archite… 13 Aug 2025 · 2 min read Building Proteins Brick by Brick: How AI Is Assembling Novel Bio-Machines Building Proteins Brick by Brick: How AI Is Assembling Novel Bio-Machines AI models like ProDomino are being developed to predict how to successfully combine different pr… 13 Aug 2025 · 2 min read AI-Driven Inverse Protein Folding: Transforming Protein Design for Next-Gen Therapeutics AI-Driven Inverse Protein Folding: Transforming Protein Design for Next-Gen Therapeutics Advanced AI models are solving the “inverse folding problem,” allowing scientists… 13 Aug 2025 · 2 min read The Protein Architect: How Generative AI Is Building the Drugs of Tomorrow The Protein Architect: How Generative AI Is Building the Drugs of Tomorrow Generative AI has evolved from predicting existing protein structures to designing entirely new… 13 Aug 2025 · 2 min read Beyond Trial and Error: AI-Driven Design of Peptide Therapeutics Beyond Trial and Error: AI-Driven Design of Peptide Therapeutics AI is transforming peptide drug discovery by replacing slow, trial-and-error methods with rapid, in silic… 11 Aug 2025 · 2 min read What If Protein Structures Could Be Designed Like LEGO? Modular Approaches in 2025 What If Protein Structures Could Be Designed Like LEGO? New AI models are enabling a modular, “LEGO-like” approach to protein design, where proteins are assembled from de… 11 Aug 2025 · 2 min read Compositional Protein Design: Building Proteins from 3D Ellipsoid Blueprints Compositional Protein Design: Building Proteins from 3D Ellipsoid Blueprints ProtComposer is a new AI model that generates protein structures based on a user-defined layo… 11 Aug 2025 · 2 min read Flow-Based Models: A New Paradigm for Protein Structure Generation Flow-Based Models: A New Paradigm for Protein Structure Generation Flow-based generative models like Proteina are an emerging alternative to diffusion models for designin… 11 Aug 2025 · 2 min read Generative AI for Protein Pocket Design: The Next Leap in Drug Discovery Generative AI for Protein Pocket Design: The Next Leap in Drug Discovery New generative AI models like PocketGen can design novel protein binding pockets from scratch, ta… 20 Aug 2025 · 3 min read Installation of RFdiffusion on MacOSX M1 architecture without GPU support Installation of RFdiffusion on MacOSX M1 architecture without GPU support Rosetta/DGL Issues: Some advanced functionalities (like DGL-based graph operations) may still fa…