ProteoAA: Residue-Aware Side-Chain Co-Evolution for All-Atom Protein Design

All-atom protein design requires coordination between backbone geometry, amino-acid identity, and side-chain packing. Yet staged design pipelines typically pass information only from backbone generation to sequence and side-chain design, leaving atomic interactions unable to guide the evolving backbone. We introduce ProteoAA, a residue-aware framework that enables bidirectional refinement through trainable adapters connecting frozen backbone and sequence–side-chain models. Backbone residue features inform sequence prediction and side-chain packing, while the resulting all-atom structure provides residue- and pair-level feedback for backbone refinement. A feedback event during diffusion incorporates this atomic information into generation, with side-chain atoms modeled conditionally on residue identity. Across unconditional protein generation, target-conditioned binder design, and side-chain packing benchmarks, Proteo-AA improves sequence–structure consistency, computational binder designability, and atomic geometry. On a standard ten-target binder benchmark, it achieves a mean designability of 31.48%, compared with 21.19% for PXDesign, and ablations support the contributions of both directions of information exchange. These results demonstrate the potential of coupling specialized pretrained models through explicit backbone–side-chain feedback for all-atom protein design.