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Cyclic peptide structure prediction and design using AlphaFold2

Author

Listed:
  • Stephen A. Rettie

    (University of Washington
    University of Washington)

  • Katelyn V. Campbell

    (University of Washington
    University of Washington)

  • Asim K. Bera

    (University of Washington)

  • Alex Kang

    (University of Washington)

  • Simon Kozlov

    (Massachusetts Institute of Technology)

  • Yensi Flores Bueso

    (University of Washington
    University of Washington
    University of Washington
    University College Cork)

  • Joshmyn Cruz

    (University of Washington)

  • Maggie Ahlrichs

    (University of Washington)

  • Suna Cheng

    (University of Washington)

  • Stacey R. Gerben

    (University of Washington)

  • Mila Lamb

    (University of Washington)

  • Analisa Murray

    (University of Washington)

  • Victor Adebomi

    (University of Washington
    Massachusetts Institute of Technology)

  • Guangfeng Zhou

    (University of Washington
    University of Washington)

  • Frank DiMaio

    (University of Washington
    University of Washington)

  • Sergey Ovchinnikov

    (Massachusetts Institute of Technology)

  • Gaurav Bhardwaj

    (University of Washington
    University of Washington
    University of Washington)

Abstract

Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here, we introduce AfCycDesign, a deep learning approach for accurate structure prediction, sequence redesign, and de novo hallucination of cyclic peptides. Using AfCycDesign, we identified over 10,000 structurally-diverse designs predicted to fold into the designed structures with high confidence. X-ray crystal structures for eight tested de novo designed sequences match very closely with the design models (RMSD

Suggested Citation

  • Stephen A. Rettie & Katelyn V. Campbell & Asim K. Bera & Alex Kang & Simon Kozlov & Yensi Flores Bueso & Joshmyn Cruz & Maggie Ahlrichs & Suna Cheng & Stacey R. Gerben & Mila Lamb & Analisa Murray & V, 2025. "Cyclic peptide structure prediction and design using AlphaFold2," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59940-7
    DOI: 10.1038/s41467-025-59940-7
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