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SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign

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SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign

AuthorsJiarui Lu†**, Yuyang Wang, Yizhe Zhang**, Jiatao Gu**, Navdeep Jaitly**, Joshua M. Susskind, Miguel Ángel Bautista

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. generative modeling in a latent space. 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. In order to effectively model the difference in sequence and structure modalities, we instantiate the framework with Transformer-based multimodal backbones that allows modality-specific processing while keeping global self-attention over both modalities. We train SimpleDesign on over 2M sequence-structure pairs achieving competitive performance across co-design and unconditional sequence/structure generation benchmarks.

September 24, 2025research area Methods and Algorithmsconference ICLR, conference ICML

Protein folding models have achieved groundbreaking results since the introduction of AlphaFold2, typically built via a combination of integrating domain-expertise into its architectural designs and training pipelines. Nonetheless, given the success of generative models across different but related problems, it is natural to question whether these architectural designs are a necessity to build performant models.


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