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    Home»DNA & Genetics»Atomically accurate de novo design of antibodies with RFdiffusion
    DNA & Genetics

    Atomically accurate de novo design of antibodies with RFdiffusion

    adminBy adminNovember 5, 2025No Comments7 Mins Read
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    Atomically accurate de novo design of antibodies with RFdiffusion
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  • Wilson, P. C. & Andrews, S. F. Tools to therapeutically harness the human antibody response. Nat. Rev. Immunol. 12, 709–719 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Paulk, A. M., Williams, R. L. & Liu, C. C. Rapidly inducible yeast surface display for antibody evolution with OrthoRep. ACS Synth. Biol. 13, 2629–2634 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lyu, X. et al. The global landscape of approved antibody therapies. Antib. Ther. 5, 233–257 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sormanni, P., Aprile, F. A. & Vendruscolo, M. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins. Proc. Natl Acad. Sci. USA 112, 9902–9907 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Liu, X. et al. Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping. Sci. Rep. 7, 41306 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545–574 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xie, X., Valiente, P. A., Lee, J. S., Kim, J. & Kim, P. M. Antibody-SGM, a score-based generative model for antibody heavy-chain design. J. Chem. Inf. Model. 64, 6745–6757 (2024).

  • Eguchi, R. R. et al. Deep generative design of epitope-specific binding proteins by latent conformation optimization. Preprint at bioRxiv https://doi.org/10.1101/2022.12.22.521698 (2022).

  • Shanehsazzadeh, A. et al. Unlocking de novo antibody design with generative artificial intelligence. Preprint at bioRxiv https://doi.org/10.1101/2023.01.08.523187 (2023).

  • Porebski, B. T. et al. Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening. Nat. Biomed. Eng. 8, 214–232 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Agarwal, A. A. et al. AlphaBind, a domain-specific model to predict and optimize antibody–antigen binding affinity. mAbs 17, 2534626 (2025).

  • Vázquez Torres, S. et al. De novo design of high-affinity binders of bioactive helical peptides. Nature 626, 435–442 (2024).

    Article 
    PubMed 
    ADS 

    Google Scholar
     

  • Sappington, I. et al. Improved protein binder design using beta-pairing targeted RFdiffusion. Preprint at bioRxiv https://doi.org/10.1101/2024.10.11.617496 (2024).

  • Cao, L. et al. Design of protein-binding proteins from the target structure alone. Nature 605, 551–560 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Gainza, P. et al. De novo design of protein interactions with learned surface fingerprints. Nature 617, 176–184 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Pacesa, M. et al. One-shot design of functional protein binders with BindCraft. Nature 646, 483–492 (2025).

  • Cutting, D., Dreyer, F. A., Errington, D., Schneider, C. & Deane, C. M. De novo antibody design with SE(3) diffusion. Preprint at arXiv https://doi.org/10.48550/arXiv.2405.07622 (2024).

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Yang, J. et al. Improved protein structure prediction using predicted interresidue orientations. Proc. Natl Acad. Sci. USA 117, 1496–1503 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Wang, J. et al. Scaffolding protein functional sites using deep learning. Science 377, 387–394 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Bennett, N. et al. Improving de novo protein binder design with deep learning. Nat. Commun. 14, 2625 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Yin, R. & Pierce, B. G. Evaluation of AlphaFold antibody–antigen modeling with implications for improving predictive accuracy. Protein Sci. 33, e4865 (2024).

  • Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Jin, B., Odongo, S., Radwanska, M. & Magez, S. Nanobodies: a review of generation, diagnostics and therapeutics. Int. J. Mol. Sci. 24, 5994 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mitchell, L. S. & Colwell, L. J. Analysis of nanobody paratopes reveals greater diversity than classical antibodies. Protein Eng. Des. Sel. 31, 267–275 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vincke, C. et al. General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold. J. Biol. Chem. 284, 3273–3284 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hunt, A. C. et al. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Sci. Transl. Med. 14, eabn1252 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ragotte, R. J. et al. De novo design of potent inhibitors of clostridial family toxins. Proc. Natl Acad. Sci. USA 122, e2509329122 (2025).

  • Rix, G. et al. Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. Science 386, eadm9073 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ravikumar, A., Arzumanyan, G. A., Obadi, M. K. A., Javanpour, A. A. & Liu, C. C. Scalable, continuous evolution of genes at mutation rates above genomic error thresholds. Cell 175, 1946–1957.e13 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Walls, A. C. et al. Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell 176, 1026–1039.e15 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yarmarkovich, M. et al. Targeting of intracellular oncoproteins with peptide-centric CARs. Nature 623, 820–827 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Sun, Y. et al. Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sci. Immunol. 8, eadj5792 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Du, H. et al. Targeting peptide antigens using a multiallelic MHC I-binding system. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02505-8 (2024).

  • Sim, M. J. W. et al. High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D. Proc. Natl Acad. Sci. USA 117, 12826–12835 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Sun, Y. et al. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. Proc. Natl Acad. Sci. USA 120, e2304055120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hitawala, F. N. & Gray, J. J. What has AlphaFold3 learned about antibody and nanobody docking, and what remains unsolved? Preprint at bioRxiv https://doi.org/10.1101/2024.09.21.614257 (2024).

  • Wang, C. et al. Proteus: pioneering protein structure generation for enhanced designability and efficiency. Preprint at bioRxiv https://doi.org/10.1101/2024.02.10.579791 (2024).

  • Yim, J. et al. Fast protein backbone generation with SE(3) flow matching. Preprint at arXiv https://doi.org/10.48550/arXiv.2310.05297 (2023).

  • Bose, J. et al. SE(3)-stochastic flow matching for protein backbone generation. In Proc. 12th International Conference on Learning Representations (ICLR, 2024).

  • Geffner, T. et al. Proteina: scaling flow-based protein structure generative models. In Proc. 13th International Conference on Learning Representations (ICLR, 2025).

  • Krishna, R. et al. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science https://doi.org/10.1126/science.adl2528 (2024).

  • Gao, S. H., Huang, K., Tu, H. & Adler, A. S. Monoclonal antibody humanness score and its applications. BMC Biotechnol. 13, 55 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dreyer, F. A., Cutting, D., Schneider, C., Kenlay, H. & Deane, C. M. Inverse folding for antibody sequence design using deep learning. Preprint at https://doi.org/10.48550/arXiv.2310.19513 (2023).

  • Prihoda, D. et al. BioPhi: a platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning. mAbs 14, 2020203 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bio, N. & Biswas, S. De novo design of epitope-specific antibodies against soluble and multipass membrane proteins with high specificity, developability, and function. Preprint at bioRxiv https://doi.org/10.1101/2025.01.21.633066 (2025).

  • Watson, J. L. Antibody training dataset for “Atomically accurate de novo design of antibodies with RFdiffusion” [data set]. Zenodo https://doi.org/10.5281/zenodo.15741710 (2025).

  • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dunbar, J. et al. SAbDab: the structural antibody database. Nucleic Acids Res. 42, D1140–D1146 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jäger, M., Gehrig, P. & Plückthun, A. The scFv fragment of the antibody hu4D5-8: evidence for early premature domain interaction in refolding. J. Mol. Biol. 305, 1111–1129 (2001).

    Article 
    PubMed 

    Google Scholar
     

  • Kawai, S., Hashimoto, W. & Murata, K. Transformation of Saccharomyces cerevisiae and other fungi. Bioeng. Bugs 1, 395–403 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Accurate Antibodies Atomically design Novo RFdiffusion
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