# Apple researchers detail SimpleDesign protein sequence-structure co-design model

_Friday, September 11, 2026 at 9:56 PM EDT · AI, Science · Latest · Tier 2 — Notable_

![Apple researchers detail SimpleDesign protein sequence-structure co-design model — Primary](https://9to5mac.com/wp-content/uploads/sites/6/2025/09/apple-simplefold-fi.jpg?quality=82&strip=all&resize=1200,628)

Apple researchers published a study describing SimpleDesign, a model that jointly generates protein sequences and 3D structures in a single end-to-end training process.

The work extends the lab's earlier SimpleFold approach, which used flow matching with general-purpose Transformer blocks to predict structure from sequence. SimpleDesign trains directly on paired amino acid sequences and 3D coordinates from more than 2 million sequence-and-structure pairs, skipping the separate tokenization stage many co-design models use.

The researchers report competitive results across co-design, structure generation, and sequence generation benchmarks, and say generated sequences were generally as good as or better than most competing multimodal models. The study states results remain limited to computer-based evaluations, with no experimental confirmation that generated proteins fold, function, or behave safely in biological systems.

## Sources

- [9to5Mac](https://9to5mac.com/2026/09/11/apple-researchers-unveil-simpledesign-a-new-ai-model-for-protein-design/)

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