MuCO: Generative Peptide Cyclization Empowered by Multi-stage Conformation Optimization

arXiv:2602.11189v2 Announce Type: replace-cross Abstract: Modeling peptide cyclization is critical for the virtual screening of candidate peptides with desirable physical and pharmaceutical properties. This task is challenging because a cyclic peptide often exhibits diverse, ring-shaped conformations, which cannot be well captured by deterministic prediction models derived from linear peptide folding. In this study, we propose MuCO (Multi-stage Conformation Optimization), a generative peptide cyclization method that models the distribution of cyclic peptide conformations conditioned on the corresponding linear peptide. In principle, MuCO decouples the peptide cyclization task into three stages: topology-aware backbone design, generative side-chain packing, and physics-aware all-atom optimization, thereby generating and optimizing conformations of cyclic peptides in a coarse-to-fine manner. This multi-stage framework enables an efficient parallel sampling strategy for conformation generation and allows for rapid exploration of diverse, low-energy conformations. Experiments on the large-scale CPSea dataset demonstrate that MuCO significantly and consistently outperforms state-of-the-art methods in physical stability, structural diversity, secondary structure recovery, and computational efficiency, making it a promising computational tool for exploring and designing cyclic peptides. The demo of the proposed method can be found at https://github.com/mianqiu00/MuCO.

Abstract:Modeling peptide cyclization is critical for the virtual screening of candidate peptides with desirable physical and pharmaceutical properties. This task is challenging because a cyclic peptide often exhibits diverse, ring-shaped conformations, which cannot be well captured by deterministic prediction models derived from linear peptide folding. In this study, we propose MuCO (Multi-stage Conformation Optimization), a generative peptide cyclization method that models the distribution of cyclic peptide conformations conditioned on the corresponding linear peptide. In principle, MuCO decouples the peptide cyclization task into three stages: topology-aware backbone design, generative side-chain packing, and physics-aware all-atom optimization, thereby generating and optimizing conformations of cyclic peptides in a coarse-to-fine manner. This multi-stage framework enables an efficient parallel sampling strategy for conformation generation and allows for rapid exploration of diverse, low-energy conformations. Experiments on the large-scale CPSea dataset demonstrate that MuCO significantly and consistently outperforms state-of-the-art methods in physical stability, structural diversity, secondary structure recovery, and computational efficiency, making it a promising computational tool for exploring and designing cyclic peptides. The demo of the proposed method can be found at this https URL.

Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI)

arXiv:2602.11189 [q-bio.BM]

(or arXiv:2602.11189v2 [q-bio.BM] for this version)

https://doi.org/10.48550/arXiv.2602.11189 Focus to learn more arXiv-issued DOI via DataCite

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MuCO: Generative Peptide Cyclization Empowered by Multi-stage Conformation Optimization

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