Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

arXiv:2605.27413v1 Announce Type: cross Abstract: Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit ligand constraints. Although continuous diffusion and flow-based models support ligand-aware design in coordinate or latent spaces, existing discrete diffusion protein language models mainly operate over sequence or