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

- Company: Apple (apple.com)
- Announced: 2026-09-11
- Category: research-paper
- Coverage: not counted
- Announcement: yes
- Group: announcements
- Source: https://machinelearning.apple.com/research/simpledesign-protein-codesign
- Record: https://forck.live/items/10301-simpledesign-a-joint-model-for-protein-sequence-and-structure-codesign
- Subject: Machine Learning Research

Apple researchers present SimpleDesign, a multi-modal protein design model that jointly generates protein sequences and structures using a single-stage end-to-end training objective, trained on over 2 million sequence-structure pairs. The model achieves competitive performance on co-design and unconditional generation benchmarks.

## Evidence

Verbatim from https://machinelearning.apple.com/research/simpledesign-protein-codesign:

> We hypothesize that this multi-stage training is not necessary to obtain performant co-design models and thus present SimpleDesign, an effective multi-modal protein design model trained directly in the data space. SimpleDesign leverages a single-stage end-to-end objective that combines discrete cross-entropy for sequences and a regression objective for structures. We train SimpleDesign on over 2M sequence-structure pairs achieving competitive performance across co-design and unconditional sequence/structure generation benchmarks.

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Record: https://forck.live/items/10301-simpledesign-a-joint-model-for-protein-sequence-and-structure-codesign
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