Data availability
Protein sequences were obtained from UniProtKB/Swiss-Prot and UniProtKB/TrEMBL (https://www.uniprot.org/, release 2023_03). Predicted protein structures were obtained from the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/). Functional annotations and keywords were obtained from InterPro (version 101.0; https://www.ebi.ac.uk/interpro/), and enzyme classification information was obtained from the ENZYME nomenclature database (https://enzyme.expasy.org/). Experimentally determined protein structures used for structural comparisons were obtained from the Protein Data Bank (PDB; https://www.rcsb.org/). UniRef100 (https://www.uniprot.org/help/uniref) was used for sequence-similarity analyses. Fluorescent-protein reference information was obtained from FPbase (https://www.fpbase.org/). The pretrained Pinal weights can be downloaded from https://huggingface.co/westlake-repl/Pinal. All the other data are available within the paper and the Supplementary Information. Source data are provided with this paper.
Code availability
Pinal is open-sourced under the Apache 2.0 license. The code repository is available at GitHub (https://github.com/westlake-repl/Denovo-Pinal). The Pinal web server is located at http://www.denovo-pinal.com/. The SaProt-T/O server, corresponding to the second component of Pinal, is linked from the Pinal web server and can also be accessed directly at http://113.45.254.183:9527/. The release of large-scale training resources for generative protein design requires careful consideration of potential dual-use biosecurity risks. In developing Pinal, the large-scale structural component of the training corpus was derived from AFDB, whose released protein-structure collection does not include viral proteomes. Accordingly, Pinal was not trained or intended for viral protein design. Nevertheless, unrestricted public release of the full pretraining corpus together with the complete training pipeline could lower the barrier for adapting similar systems to sensitive biological datasets. To mitigate this risk, these full-scale training resources were provided only under confidential access for editorial and peer review assessment. Because they will not be publicly released in full, and to support transparency and reproducibility, we instead provide public access to the inference code, evaluation code, model usage instructions, trained model weights and the web server, in line with common release practices for large-scale protein foundation models such as AlphaFold69,74, ESM338 and ESMFold68. Additional information about the composition, sources, filtering strategy, and construction of the training corpus is provided in the Methods and Supplementary Information.
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Acknowledgements
We thank N. Li and the Westlake HPC Center for providing computing resources and technical support. We also thank A. Gitter, H. Liu and S. Ovchinnikov for their suggestions, which helped improve the manuscript. We acknowledge the support of the Biosciences Central Research Facility (BioCRF (GZ)) and the Bioresearch Lab at the Hong Kong University of Science and Technology (Guangzhou). Their assistance with equipment and facility access, experimental procedures and material characterization was essential to this study. Finally, we thank Y. Mao for assistance with the H-protein-R2 validation experiments.
Funding
This work was supported by the National Natural Science Foundation of China (grant nos. 62576286 and 32471547), the National Key Research and Development Program of China (grant no. 2022ZD0115100), the Guangdong Education Department (grant no. 2023ZDZX2073), the Guangzhou-HKUST(GZ) Joint Funding Program (grant no. 2025A03J3791), the Nansha Key Science and Technology Project (no. 2023ZD015), and the Zhejiang Province Leading Geese Plan (grant no. 2025C01094), the Guangdong S&T Program (2024B1111140001) and the Shenzhen Science and Technology Program (RCJC20221008092810021).
Author information
Author notes
These authors contributed equally: Fengyuan Dai, Shiyang You
Authors and Affiliations
School of Engineering, Westlake University, Hangzhou, China
Fengyuan Dai, Yudian Zhu, Xibin Zhou, Jin Su, Yuliang Fan, Qingsong Tan, Hui Qian, Zhe Zhang, Chenchen Han, Yajie Wang, Anping Zeng, Chunjun Zhan, Jianming Liu & Fajie Yuan
Zhejiang University, Hangzhou, China
Fengyuan Dai
Bioscience and Biomedical Engineering Thrust, Systems Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
Shiyang You, Xiaoxiao Ma, Xianjun Deng, Letong Yu & Hongyuan Lu
State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
Yuan Gao, Lihao Fu & Tong Si
School of Life Sciences, Westlake University, Hangzhou, China
Chentong Wang, Yan He, Yitao Ke, Xing Chang & Longxing Cao
Shanghai Zelixir Biotech, Shanghai, China
Liangzhen Zheng & Sheng Wang
State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, China
Yuan Ji, Kexin Hao & Jing Zhao
Zhejiang Key Laboratory of Low-Carbon Intelligent Synthetic Biology, School of Engineering, Westlake University, Hangzhou, China
Anping Zeng, Jianming Liu & Fajie Yuan
Department of Biochemistry, University of Washington, Seattle, WA, USA
Shunzhi Wang
Authors
- Fengyuan Dai
- Shiyang You
- Yudian Zhu
- Yuan Gao
- Lihao Fu
- Xibin Zhou
- Jin Su
- Chentong Wang
- Yuliang Fan
- Qingsong Tan
- Xiaoxiao Ma
- Xianjun Deng
- Letong Yu
- Hui Qian
- Yan He
- Yitao Ke
- Zhe Zhang
- Chenchen Han
- Xing Chang
- Liangzhen Zheng
- Sheng Wang
- Yuan Ji
- Kexin Hao
- Longxing Cao
- Yajie Wang
- Anping Zeng
- Shunzhi Wang
- Chunjun Zhan
- Jing Zhao
- Tong Si
- Jianming Liu
- Hongyuan Lu
- Fajie Yuan
Contributions
F.Y., F.D. and H.L. conceived the study. F.Y. led the overall project design and computational framework development. H.L., J.L. and T.S. led and supervised the biological experiments. F.D. and S.Y. carried out the main research. F.Y. and F.D. designed the Pinal framework and data-scaling strategy. F.D. implemented and trained the Pinal model. Y.F. and Q.T. performed some model evaluation. Shunzhi Wang, X.C. and Y.W. contributed to discussions and provided insightful feedback. Y.Z., A.Z. and J.L. contributed to the H-protein validation experiments. Y.G., L.F. and T.S. contributed to the GFP validation experiments. X.M., L.Y., S.Y., Z.Z., C.Z. and H.L. contributed to the PETase validation experiments. X.D., S.Y., Y.J., K.H., J.Z. and H.L. contributed to the ADH validation experiments. S.Y., H.Q., Y.K., C.W., Y.W. and L.C. performed the soluble protein expression experiments. Y.H., L.Z. and Sheng Wang contributed to early-stage exploratory experiments. X.Z., J.S. and C.H. collected and curated the datasets used in this study. F.Y., F.D., H.L., S.Y., J.L. and T.S. wrote the paper, and all authors read the paper.
Corresponding authors
Correspondence to Tong Si, Jianming Liu, Hongyuan Lu or Fajie Yuan.
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Extended data figures and tables
Extended Data Fig. 1 Detailed architectures of the Pinal generative modules.
a: T2struct translates natural language descriptions into structural (3Di) token sequences. A text encoder first generates the text representation according to the function prompt. This representation is then used to guide the T2struct decoder block, which autoregressively predicts the sequence of 3Di structural tokens. The detailed view (right) illustrates the internal composition of each decoder block (repeated N times), consisting of three sequential sub-modules: a structural context module (implemented via multi-head self-attention) to process the generated structural sequence, a text-conditioning module (employing multi-head cross-attention) to integrate guidance from the text representation, and a feature refinement network (a pointwise feed-forward layer) for further feature processing. Layer normalization is applied within each sub-module. b: The SaProt-T module, which designs an amino acid sequence based on both the structural input and the text prompt. A semantic projector maps the text representation into the same embedding space as the structural tokens. This projected text vector is prepended to the structural token embeddings to form a text-protein joint representation. This joint representation is then processed by the SaProt-T block, repeated N times, to predict the final amino acid sequence.
Extended Data Fig. 2 Text conditioning is crucial for the sequence design module.
a: Ablation study comparing the performance of SaProt-T and SaProt-O (760M parameters) against the original SaProt (650M), the ProstT5 baseline, and the scaled SaProt-T-T5xxl_encoder (~5B). Performance is evaluated based on textual alignment (x-axis) and predicted foldability (y-axis). The results show that our text-conditioned models (SaProt-T/O) outperform the original SaProt and the ProstT5 baseline, particularly in maintaining structural foldability. The size of each bubble corresponds to the number of model parameters, as indicated in the legend. b: Composition of the omni-modal training strategy for the SaProt-O model. This strategy involves a varied combination of masking applied to the amino acid (AA) sequence, the structural tokens, and the text prompt to train a flexible, multi-purpose design model. The left panel details the distribution of structural token masking (no, partial, or full masking) under two different AA masking conditions. The right panel shows that the text prompt is masked in 40% of the training examples.
Extended Data Fig. 3 Determining the optimal number of sampling candidates (K).
Performance of the top-ranked Pinal designs on the “hard” test set as a function of the number of sampled candidates (K). For each value of K, we generate K candidates, rank them by their joint log-probability, and then evaluate the top-ranked design. Left panel: textual alignment, measured by Max. and Mean Seq. ProTrek score. Right panel: predicted structural plausibility, measured by ESMFold pLDDT. Both textual alignment and foldability improve as K increases from 5 to 50. Further increasing K to 100 yields only marginal gains (or a slight decrease in ProTrek score) while substantially increasing computational cost. Based on this analysis, K = 50 is used as the standard setting for all experiments, offering a robust balance between design performance and inference efficiency.
Extended Data Fig. 4 ProTrek score is a robust and discriminative metric for both text-sequence and text-structure alignment.
The figure validates the ProTrek score’s performance using a test set of 1,000 protein-text pairs from Swiss-Prot. The top row (a-c) evaluates the text-to-sequence score (Seq. ProTrek), while the bottom row (d-f) evaluates the text-to-structure score (Struc. ProTrek). (a, d) Box plots show the distribution of ProTrek scores for proteins paired with their original descriptions, LLM-paraphrased descriptions, and randomly assigned (mismatched) descriptions. For both sequence and structure, the scores for original and paraphrased text are high and similar, while scores for random text are lower, demonstrating the metric’s discriminative power. Box plots show the median (centre line), 25th-75th percentiles (box), the most extreme values within 1.5 × the interquartile range (whiskers), and outliers (points). (b, e) Scatter plots comparing the scores of original versus paraphrased descriptions for each protein. The strong linear relationship, confirmed by a Spearman’s rank correlation coefficient (ρ) of > 0.98 for both sequence and structure, demonstrates that the metric is robust to variations in wording and captures core semantic meaning. (c, f) Scatter plots comparing the scores of original versus randomly assigned descriptions. The near-zero correlations (ρ ≈ 0) further confirm that the ProTrek score is a valid metric that reliably distinguishes between relevant and irrelevant protein-text pairings. The original ProTrek study also demonstrated that its score selectively responds to biologically relevant keywords while ignoring non-functional terms. Building on this capability, a recent benchmark paper48 adopted ProTrek as a key metric for evaluating the alignment between protein sequences and their textual descriptions.
Extended Data Fig. 5 The three-phase training improves model performance and mitigates sequence repetition.
a, Performance of the 15.5B T2struct model on the “hard” test set across three distinct training phases. Phase 1 (320k steps) represents initial training; Phase 2 (625k steps) incorporates data filtering by ProTrek score; Phase 3 (740k steps) is a final fine-tuning step on higher-quality data filtered to exclude low-pLDDT scores and high token repetition. The plots demonstrate that the third phase improves protein foldability, while incurring only a minor, acceptable trade-off in textual alignment (ProTrek score). b, Analysis of the sequence repetition phenomenon that motivated the third training phase. The left panel shows that the model after Phase 2 exhibited a high rate of amino acid repetition (≥5) (e.g.,“AAAAA”) at 60.2%, far exceeding that of natural proteins (UniProt, 4.0%). The final model after Phase 3 substantially reduces this rate to 35.3%. The right panel illustrates the effectiveness of the Phase 3 training data-filtering strategy. The high rate of Foldseek token repetition in the Phase 2 model’s outputs (91%) correlates with the high rate found in the AFDB training data (90%). The refined training strategy after Phase 3 successfully reduces the rate of token repetition greater than 10 to just 4%, thereby substantially resolving the Foldseek structure token repetition issue.
Extended Data Fig. 6 Detailed performance analysis across diverse protein function descriptions.
The figure evaluates Pinal’s design performance across 17 distinct functional categories curated from Swiss-Prot. Left panel: Analysis of textual alignment, measured by the maximum sequence ProTrek score (n = 50 functional prompts per subsection). The performance of Pinal’s top-ranked design (blue) is compared against a random baseline (light grey) and the ground-truth protein (dark grey) for each category. Pinal consistently outperforms the random baseline across all categories and approaches ground-truth performance, demonstrating robust language understanding. Right panel: Predicted structural plausibility of the corresponding Pinal-designed proteins, measured by ESMFold pLDDT (n = 250 Pinal-designed proteins per subsection). The results indicate that Pinal generates proteins with high predicted foldability (median pLDDT is typically > 80) across all functional description types, from concrete categories like “Protein names” to more abstract ones like “Disruption phenotype”. Box plots show the median (centre line), 25th-75th percentiles (box), the most extreme values within 1.5 × the interquartile range (whiskers), and outliers (points).
Extended Data Fig. 7 Computational design, screening, and characterization of pinalGFP.
a, Flowchart illustrating the multi-tiered computational filtering strategy applied to the initial Pinal-generated sequences. This pipeline culminated in the selection of 29 candidates for experimental validation. b, Multiple sequence alignment of pinalGFP, avGFP, and esmGFP-b8. The alignment highlights the substantial sequence divergence of pinalGFP from both the natural protein and the other synthetic variant. c, Normalized fluorescence excitation (dashed lines, λem = 510 nm) and emission (solid lines, λex = 460 nm) spectra of pinalGFP (blue) and avGFP (green). d, Size-exclusion chromatography profiles of purified GFP variants on a Superdex 200 column. Elution volumes reflected their oligomeric states in solution: avGFP was predominantly dimeric, whereas pinalGFP exhibited a more complex profile dominated by higher-order multimers.
Extended Data Fig. 8 Computational screening pipeline and pNP standard curve for pinalPETase identification.
a, Flowchart illustrating the multi-tiered screening strategy used to identify the active PETase candidate from the initial pool of Pinal-generated sequences. Candidates were first filtered on the basis of predicted structural quality (ESMFold pLDDT > 80, PAE < 7) and text–protein alignment (ProTrek score > 15), yielding 2,416 sequences. The top 94 candidates, ranked by ProTrek score, were then subjected to esterase activity screening using the p-nitrophenyl butyrate (pNPB) assay. This workflow led to the identification of a single standout variant, pinalPETase36, which was subsequently advanced to PET hydrolysis validation. The inset shows the predicted active-site architecture of pinalPETase36. b, Standard curve for p-nitrophenol (pNP) used for quantification of esterase activity in the pNPB assay. Absorbance at 410 nm was plotted against pNP concentration, showing a strong linear relationship (R2 = 0.9947). Data are shown as mean ± s.d. (n = 3 independent measurements).
Extended Data Fig. 9 Computational design pipeline and analytical method for Pinal-designed ADHs.
a, Flowchart of the computational screening and selection process for ADH candidates. From an initial library of 2,500 generated sequences, 1,639 candidates passing the feasibility filters based on structural confidence (ESMFold pLDDT > 80, PAE < 7) were identified, from which 1,000 sequences were randomly retained for downstream prioritization. From these, eight diverse candidates representing different ADH subfamilies were selected, leading to five successfully validated enzymes. b, UMAP of alcohol dehydrogenase (ADH) sequences. A total of 1,000 Pinal-designed ADH sequences (blue) were analysed together with natural ADH sequences from Swiss-Prot (gray; EC 1.1.1.1). Sequence embeddings were generated using ESM2-650M and projected into two dimensions by UMAP. The Pinal-designed sequences span a substantial region of the natural ADH sequence space. c, Representative HPLC chromatograms of derivatized acetaldehyde standards, corresponding to the product of the ADH-catalyzed reaction. Acetaldehyde standards at 0.1, 0.2, and 0.5 mM showed a consistent retention time of approximately 7.3 min.
Extended Data Fig. 10 Computational design, screening, and mechanistic analysis of Pinal-designed H-proteins.
a, Flowchart illustrating the computational design and screening pipeline for H-protein candidates. The initial generation was filtered to yield approximately 1,000 sequences that simultaneously satisfied the protein-text alignment criterion (ProTrek score > 15) and the sequence-divergence criterion ( < 60% sequence identity to known homologs). From this pool, 20 highly ranked candidates were selected, identifying five sequences with experimentally confirmed activity. b, Initial activity screening of 14 soluble Pinal-designed H-proteins compared to the native E. coli H-protein (‘ecH’). Glycine synthesis was measured after a 2 h reaction in a reconstituted Glycine Cleavage System (GCS). Data are shown as mean ± s.d. (n = 3 biologically independent reactions). c-f, Molecular dynamics (MD) simulations comparing the conformational dynamics of the lipoamide arm in the top-performing ‘pinalH02’ and the native ‘ecH’. c, Trajectory of the distance between the Cδ atom of Glu27 in ‘pinalH02’ and the nitrogen atom of the lipoamide arm over 500 ns. The plot shows that the arm frequently samples extended conformations far from the protein core. d, Corresponding distance trajectory for ‘ecH’, plotting the distance between the Cδ atom of Glu12 and the arm’s nitrogen atom over 500 ns. The arm remains stably sequestered close to the protein body. e, A representative snapshot of the ‘pinalH02’ conformation at 200 ns, illustrating the solvent-exposed lipoamide arm. f, A representative snapshot of ‘ecH’ at 200 ns, showing the aminomethyl lipoate arm locked within the protein’s hydrophobic cavity.
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Dai, F., You, S., Zhu, Y. et al. Programmable design of functional proteins from natural language. Nature (2026). https://doi.org/10.1038/s41586-026-11205-z
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DOI: https://doi.org/10.1038/s41586-026-11205-z