Year: 2026
Type: preprint
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.
Authors: Qirui Deng, Mingyuan Xu, Hongming Chen, Jinping Lei
Language: English
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7221449544