Atomically Accurate De Novo Design Of Antibodies With RFdiffusion

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.Nature620, 1089–1100 (2023).

PubMed و Wilson, و P. – تفاصيل مهمة

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).

C. و antibody و Paulk, – تفاصيل مهمة

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. USA112, 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).

design و of و Sci. – تفاصيل مهمة

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).

J. و for و PubMed – تفاصيل مهمة

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

Shanehsazzadeh, A. et al. Unlocking de novo antibody design with generative artificial intelligence. Preprint atbioRxivhttps://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 

et و al. و Shanehsazzadeh, – تفاصيل مهمة

Agarwal, A. A. et al. AlphaBind, a domain-specific model to predict and optimize antibody–antigen binding affinity.mAbs17, 2534626 (2025).

Vázquez Torres, S. et al. De novo design of high-affinity binders of bioactive helical peptides.Nature626, 435–442 (2024).

Article 
PubMed 
ADS 

Google Scholar 

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

et و al. و design – تفاصيل مهمة

Cao, L. et al. Design of protein-binding proteins from the target structure alone.Nature605, 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.Nature617, 176–184 (2023).

Article 
CAS 
PubMed 
PubMed Central 
ADS 

Google Scholar 

PubMed و Article و CAS – تفاصيل مهمة

Pacesa, M. et al. One-shot design of functional protein binders with BindCraft.Nature646, 483–492 (2025).

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

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold.Nature596, 583–589 (2021).

Article 
CAS 
PubMed 
PubMed Central 
ADS 

Google Scholar 

D., و C. و with – تفاصيل مهمة

Yang, J. et al. Improved protein structure prediction using predicted interresidue orientations.Proc. Natl Acad. Sci. USA117, 1496–1503 (2020).

Article 
CAS 
PubMed 
PubMed Central 
ADS 

Google Scholar 

Wang, J. et al. Scaffolding protein functional sites using deep learning.Science377, 387–394 (2022).

Article 
CAS 
PubMed 
PubMed Central 
ADS 

Google Scholar 

PubMed و Article و CAS – تفاصيل مهمة

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.Nature630, 493–500 (2024).

PubMed و of و AlphaFold – تفاصيل مهمة

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).

& و S. و of – تفاصيل مهمة

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).

C. و et و al. – تفاصيل مهمة

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. USA122, e2509329122 (2025).

Rix, G. et al. Continuous evolution of user-defined genes at 1 million times the genomic mutation rate.Science386, eadm9073 (2024).

Article 
CAS 
PubMed 

Google Scholar 

of و et و al. – تفاصيل مهمة

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.Cell175, 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.Cell176, 1026–1039.e15 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

PubMed و Article و CAS – تفاصيل مهمة

Yarmarkovich, M. et al. Targeting of intracellular oncoproteins with peptide-centric CARs.Nature623, 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 

PubMed و Article و CAS – تفاصيل مهمة

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. USA117, 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. USA120, e2304055120 (2023).

et و al. و Proc. – تفاصيل مهمة

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 atbioRxivhttps://doi.org/10.1101/2024.09.21.614257 (2024).

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

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

J. و and و Preprint – تفاصيل مهمة

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

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

Krishna, R. et al. Generalized biomolecular modeling and design with RoseTTAFold All-Atom.Sciencehttps://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).

et و al. و and – تفاصيل مهمة

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.mAbs14, 2020203 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar 

antibody و for و deep – تفاصيل مهمة

Bio, N. & Biswas, S. De novo design of epitope-specific antibodies against soluble and multipass membrane proteins with high specificity, developability, and function. Preprint atbioRxivhttps://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).Zenodohttps://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 

of و PubMed و Watson, – تفاصيل مهمة

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 

Article و PubMed و Google – تفاصيل مهمة

Kawai, S., Hashimoto, W. & Murata, K. Transformation ofSaccharomyces cerevisiaeand other fungi.Bioeng. Bugs1, 395–403 (2010).

Article 
PubMed 
PubMed Central 

Google Scholar