PeTFlow: Flow-Matching Based All-Atom Peptide Design through Side-Chain State Tokenization

Authors

Deng, Q., Xu, M., Chen, H., Lei, J.

Abstract

Peptide offers a powerful modality for targeting protein-protein interfaces, yet their computational design remains challenging because sequence identity, backbone geometry and side-chain packing must be optimized simultaneously within a three-dimensional pocket constrained environment. Here we present PeTFlow, a pocket-conditioned all-atom peptide co-design framework that rationalizes this constrained design problem through discrete side-chain state tokenization. In PeTFlow, each residue is represented as a chemically compatible state token, enabling unified modeling of peptide sequence, conformation and all-atom interface geometry. PeTFlow achieved superior generation quality on peptide-design benchmarks and can further be applied to therapeutically relevant peptide drug design.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 12 Oct 2026.

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