Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
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 structure tokens without direct small-molecule conditioning. We introduce \textbf{ProtLiD$^2$}, a \textbf{Prot}ein \textbf{L}igand-conditioned \textbf{D}iscrete \textbf{D}iffusion model for protein sequence-structure co-design. ProtLiD$^2$ jointl...
| Authors | Chen Wei, Fanding Xu, Minghao Sun et al. |
|---|---|
| Primary category | q-bio.BM |
| Published | 15 May 2026 |
| Last updated at source | 15 May 2026 |
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