% Key papers for Diffusion for protein and antibody design (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{neurips2022_antigen_65760,
  title = {{Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/55183},
}

@inproceedings{icml2023_se_42862,
  title = {{SE(3) diffusion model with application to protein backbone generation}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2023},
  url = {https://icml.cc/virtual/2023/poster/24926},
}

@inproceedings{neurips2023_graph_69772,
  title = {{Graph Denoising Diffusion for Inverse Protein Folding}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/70170},
}

@inproceedings{icml2024_proteus_44030,
  title = {{Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34422},
}

@inproceedings{icml2024_diffusion_44249,
  title = {{Diffusion Language Models Are Versatile Protein Learners}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34203},
}

@inproceedings{icml2024_protein_44757,
  title = {{Protein Conformation Generation via Force-Guided SE(3) Diffusion Models}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/33695},
}

@inproceedings{neurips2023_pre_69727,
  title = {{Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/70211},
}

@inproceedings{icml2025_diffusion_49036,
  title = {{Diffusion on Language Model Encodings for Protein Sequence Generation}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/43588},
}

@inproceedings{neurips2024_antigen_71338,
  title = {{Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/95910},
}

@inproceedings{iclr2025_dplm_80850,
  title = {{DPLM-2: A Multimodal Diffusion Protein Language Model}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/30917},
}

@inproceedings{neurips2024_msagpt_73957,
  title = {{MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/93555},
}

@inproceedings{iclr2025_proteina_82252,
  title = {{Proteina: Scaling Flow-based Protein Structure Generative Models}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/29538},
}

@inproceedings{icml2024_floating_43798,
  title = {{Floating Anchor Diffusion Model for Multi-motif Scaffolding}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34654},
}

@inproceedings{neurips2025_generative_76440,
  title = {{Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=JPjMXgQQxk},
}

@inproceedings{iclr2025_retrieval_82611,
  title = {{Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/29186},
}

@inproceedings{icml2025_cfp_46638,
  title = {{CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45932},
}

@inproceedings{icml2025_domain_48327,
  title = {{Domain-Adapted Diffusion Model for PROTAC Linker Design Through the Lens of Density Ratio in Chemical Space}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44288},
}

@inproceedings{icml2026_td3b_51951,
  title = {{TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=RNuC8Nj6rD},
}

@inproceedings{icml2026_towards_53669,
  title = {{Towards A Generative Protein Evolution Machine with DPLM-Evo}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=hcFVDmmb0J},
}

@inproceedings{icml2026_cross_54125,
  title = {{Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=mAusAlRZ0a},
}

@inproceedings{neurips2025_repurposing_76699,
  title = {{Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=M96edY67nS},
}

@inproceedings{neurips2025_ambient_77804,
  title = {{Ambient Proteins - Training Diffusion Models on Noisy Structures}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=Xll01vw606},
}

@inproceedings{iclr2026_scalable_86447,
  title = {{Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=Q1JpRZkR3S},
}

@inproceedings{iclr2026_constrained_88251,
  title = {{Constrained Diffusion for Protein Design with Hard Structural Constraints}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=kkvqVRu2Zy},
}