ArticleNature communications2025
Protein sequence modelling with Bayesian flow networks.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Recombinant Protein Drugs: A 2025 Update.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2026Review
- Sampling out-of-distribution chemical spaces via Bayesian flow.Journal of cheminformatics · 2026Article
- Peptides from 'Vaina Morada' Black Bean Inhibit α-Amylase and α-Glucosidase: A Combined In Silico-In Vitro Study.Foods (Basel, Switzerland) · 2025Article
- ProDualNet: dual-target protein sequence design method based on protein language model and structure model.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exploring the vast and largely uncharted territory of amino acid sequences is crucial for understanding complex protein functions and the engineering of novel therapeutic proteins. Whilst generative machine learning has advanced protein sequence modelling, no existing approach is proficient in both unconditional and conditional generation. In this work, we propose that Bayesian Flow Networks (BFNs), a recently introduced framework for generative modelling, can address these challenges. We present ProtBFN, a 650M parameter model trained on protein sequences curated from UniProtKB, which generates natural-like, diverse, structurally coherent, and novel protein sequences, significantly outperforming leading autoregressive and discrete diffusion models. Further, we fine-tune ProtBFN on heavy chains from the Observed Antibody Space to obtain an antibody-specific model, AbBFN, which we use to evaluate zero-shot conditional generation capabilities. AbBFN is found to be competitive with or better than antibody-specific BERT-style models when applied to predicting individual framework or complimentary determining regions.
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Registered trials
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