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

@inproceedings{neurips2018_generative_57171,
  title = {{Generative modeling for protein structures}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2018},
  url = {https://nips.cc/virtual/2018/poster/11721},
}

@inproceedings{iclr2023_diffusion_32073,
  title = {{Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/11916},
}

@inproceedings{iclr2019_learning_28833,
  title = {{Learning Protein Structure with a Differentiable Simulator}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2019},
  url = {https://iclr.cc/virtual/2019/poster/959},
}

@inproceedings{icml2024_alphafold_45514,
  title = {{AlphaFold Meets Flow Matching for Generating Protein Ensembles}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/32938},
}

@inproceedings{aaai2016_must_104720,
  title = {{MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-Based Protein Structure Prediction}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2016},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/10007},
}

@inproceedings{icml2023_generating_41556,
  title = {{Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2023},
  url = {https://icml.cc/virtual/2023/poster/24633},
}

@inproceedings{icml2022_proximal_41050,
  title = {{Proximal Exploration for Model-guided Protein Sequence Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/17763},
}

@inproceedings{icml2021_fold2seq_39358,
  title = {{Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2021},
  url = {https://icml.cc/virtual/2021/poster/9593},
}

@inproceedings{iclr2024_se_35093,
  title = {{SE(3)-Stochastic Flow Matching for Protein Backbone Generation}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/17980},
}

@inproceedings{iclr2023_protein_33198,
  title = {{Protein Sequence and Structure Co-Design with Equivariant Translation}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/10731},
}

@inproceedings{icml2023_chemically_41659,
  title = {{Chemically Transferable Generative Backmapping of Coarse-Grained Proteins}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2023},
  url = {https://icml.cc/virtual/2023/poster/24126},
}

@inproceedings{icml2024_generative_45195,
  title = {{Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/33257},
}

@inproceedings{icml2025_p_49099,
  title = {{P(all-atom) Is Unlocking New Path For Protein Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/43525},
}

@inproceedings{iclr2024_str2str_33887,
  title = {{Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19188},
}

@inproceedings{aaai2025_bridging_8310,
  title = {{Bridging Sequence-Structure Alignment in RNA Foundation Models}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/35500},
}

@inproceedings{icml2024_rnaflow_45173,
  title = {{RNAFlow: RNA Structure \& Sequence Design via Inverse Folding-Based Flow Matching}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/33279},
}

@inproceedings{icml2025_sidechain_46606,
  title = {{Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45963},
}

@inproceedings{cvpr2023_fff_20961,
  title = {{FFF: Fragment-Guided Flexible Fitting for Building Complete Protein Structures}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2023},
  url = {https://cvpr.thecvf.com/virtual/2023/poster/22761},
}

@inproceedings{icml2025_inverse_48710,
  title = {{Inverse problems with experiment-guided AlphaFold}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/43912},
}

@inproceedings{neurips2022_exploring_65049,
  title = {{Exploring evolution-aware \& -free protein language models as protein function predictors}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/54277},
}

@inproceedings{neurips2024_sequence_73970,
  title = {{Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Generation}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/93544},
}

@inproceedings{neurips2025_multiscale_77366,
  title = {{Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=T3DF4yxcPz},
}

@inproceedings{icml2024_surfpro_44753,
  title = {{SurfPro: Functional Protein Design Based on Continuous Surface}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/33699},
}

@inproceedings{neurips2024_full_71476,
  title = {{Full-Atom Peptide Design with Geometric Latent Diffusion}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/95784},
}

@inproceedings{iclr2025_fast_80576,
  title = {{Fast Uncovering of Protein Sequence Diversity from Structure}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/32112},
}

@inproceedings{iclr2025_proteinbench_81217,
  title = {{ProteinBench: A Holistic Evaluation of Protein Foundation Models}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/30553},
}

@inproceedings{iclr2026_simplefold_84260,
  title = {{SimpleFold: Folding Proteins is Simpler than You Think}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=0j0MmK7EMA},
}

@inproceedings{aaai2025_cryodomain_8573,
  title = {{CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/31987},
}

@inproceedings{aaai2025_prifold_10352,
  title = {{PriFold: Biological Priors Improve RNA Secondary Structure Predictions}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/32080},
}

@inproceedings{aaai2025_dyab_11331,
  title = {{dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/32061},
}

@inproceedings{icml2024_full_43494,
  title = {{Full-Atom Peptide Design based on Multi-modal Flow Matching}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34958},
}