# SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign

DevFeed: [SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign](<https://devfeed.tech/articles/simpledesign-a-joint-model-for-protein-sequence-and-structure-codesign-6735.md>)

Original publisher: [Read original article](<https://machinelearning.apple.com/research/simpledesign-protein-codesign>)

Published: 2026-09-11T00:00:00Z

Content type: article

Language: en

Sources: [Apple Machine Learning Research](<https://devfeed.tech/sources/apple-machine-learning-research.md>)

Topics: [multimodal](<https://devfeed.tech/topics/multimodal.md>), [Transformer](<https://devfeed.tech/topics/transformer.md>), [datasets](<https://devfeed.tech/topics/datasets.md>)

Tags: [benchmarks](<https://devfeed.tech/tags/benchmarks.md>), [drug-discovery](<https://devfeed.tech/tags/drug-discovery.md>), [generation](<https://devfeed.tech/tags/generation.md>), [model](<https://devfeed.tech/tags/model.md>), [multimodal](<https://devfeed.tech/tags/multimodal.md>), [training](<https://devfeed.tech/tags/training.md>)

## AI overview

SimpleDesign is a single-stage, end-to-end multimodal generative model for jointly designing protein sequences and three-dimensional structures. It uses Transformer-based multimodal backbones, trains directly in data space on more than 2 million sequence-structure pairs, and achieves competitive results on co-design and unconditional generation benchmarks.

## Source excerpt

Proteins are fundamental to biological processes, with their function determined by the complex interplay between the amino acid sequence and the three-dimensional structure. Developing generative models capable of understanding this intrinsically multi-modal relationship is crucial for fields like drug discovery and protein engineering. Existing models often rely on a multi-stage training process where autoencoders that tokenize data into latent representations are trained in a first stage. Secondly, a generative model is trained on the latent representation of the autoencoder(s), i.e...