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@ARTICLE{Sappington:646221,
      author       = {Sappington, Isaac and Toul, Martin and Lee, David S. and
                      Robinson, Stephanie A. and Goreshnik, Inna and McCurdy,
                      Clara and Chan, Tung Ching and Buchholz, Nic and Huang,
                      Buwei and Vafeados, Dionne and Garcia-Sanchez, Mariana and
                      Roullier, Nicole and Glögl, Matthias and Kim, Christopher
                      J. and Watson, Joseph L. and Torres, Susana Vázquez and
                      Verschueren, Koen H. G. and Verstraete, Kenneth and Hinck,
                      Cynthia S. and Benard-Valle, Melisa and Coventry, Brian and
                      Sims, Jeremiah Nelson and Ahn, Green and Wang, Xinru and
                      Hinck, Andrew P. and Jenkins, Timothy P. and Ruohola-Baker,
                      Hannele and Banik, Steven M. and Savvides, Savvas N. and
                      Baker, David},
      title        = {{I}mproved protein binder design using β-pairing targeted
                      {RF}diffusion},
      journal      = {Nature Communications},
      volume       = {17},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Springer Nature},
      reportid     = {PUBDB-2026-00766},
      pages        = {1101},
      year         = {2026},
      abstract     = {Designing proteins that bind with high affinity to
                      hydrophilic protein target sites remains a challenging
                      problem. Here we show that RFdiffusion can be conditioned to
                      generate protein scaffolds that form geometrically matched
                      extended β-sheets with target protein edge β-strands in
                      which polar groups on the target are complemented with
                      hydrogen bonding groups on the design. We use this approach
                      to design binders against edge-strand target sites on KIT,
                      PDGFRɑ, ALK-2, ALK-3, FCRL5, NRP1, and α-CTX, and obtain
                      higher (pM to mid nM) affinities and success rates than
                      unconditioned RFdiffusion. Despite sharing β-strand
                      interactions, designs have high specificity, reflecting the
                      precise customization of interacting β-strand geometry and
                      additional designed binder-target interactions. A binder-KIT
                      co-crystal structure is nearly identical to the design
                      model, confirming the accuracy of the design approach. The
                      ability to robustly generate binders to the hydrophilic
                      interaction surfaces of exposed β-strands considerably
                      increases the range of computational binder design.},
      cin          = {EMBL-User},
      ddc          = {500},
      cid          = {I:(DE-H253)EMBL-User-20120814},
      pnm          = {6G3 - PETRA III (DESY) (POF4-6G3)},
      pid          = {G:(DE-HGF)POF4-6G3},
      experiment   = {EXP:(DE-H253)P-P13-20150101},
      typ          = {PUB:(DE-HGF)16},
      doi          = {10.1038/s41467-025-67866-3},
      url          = {https://bib-pubdb1.desy.de/record/646221},
}