% Key papers for Protein interface and docking prediction (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{neurips2022_tankbind_64707,
  title = {{TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/54430},
}

@inproceedings{aaai2020_caster_100239,
  title = {{CASTER: Predicting Drug Interactions with Chemical Substructure Representation}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2020},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/5412},
}

@inproceedings{icml2022_equibind_40505,
  title = {{EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/18361},
}

@inproceedings{cvpr2021_fast_17008,
  title = {{Fast End-to-End Learning on Protein Surfaces}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2021},
}

@inproceedings{neurips2019_end_58214,
  title = {{End-to-End Learning on 3D Protein Structure for Interface Prediction}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2019},
  url = {https://nips.cc/virtual/2019/poster/14452},
}

@inproceedings{iclr2023_rotamer_32796,
  title = {{Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/12198},
}

@inproceedings{iclr2022_independent_31078,
  title = {{Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2022},
  url = {https://iclr.cc/virtual/2022/poster/7055},
}

@inproceedings{neurips2023_diffpack_69674,
  title = {{DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/70263},
}

@inproceedings{iclr2023_e3bind_33273,
  title = {{E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/11644},
}

@inproceedings{aaai2024_psc_6907,
  title = {{PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/27784},
}

@inproceedings{iclr2020_energy_29579,
  title = {{Energy-based models for atomic-resolution protein conformations}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2020},
  url = {https://openreview.net/forum?id=S1e_9xrFvS},
}

@inproceedings{neurips2023_predicting_67219,
  title = {{Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/72495},
}

@inproceedings{iclr2026_sair_88758,
  title = {{SAIR: Enabling Deep Learning for Protein-Ligand Interactions with a Synthetic Structural Dataset}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=qgk2F6jxH4},
}

@inproceedings{neurips2025_neuralplexer3_75757,
  title = {{NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=BlLAmMFEzJ},
}

@inproceedings{icml2024_harmonic_44630,
  title = {{Harmonic Self-Conditioned Flow Matching for joint Multi-Ligand Docking and Binding Site Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/33822},
}

@inproceedings{aaai2025_4d_7875,
  title = {{4D Diffusion for Dynamic Protein Structure Prediction with Reference and Motion Guidance}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/31984},
}

@inproceedings{icml2024_ppflow_43554,
  title = {{PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34898},
}

@inproceedings{icml2024_re_44371,
  title = {{Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34081},
}

@inproceedings{iclr2024_rigid_35699,
  title = {{Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/17374},
}

@inproceedings{neurips2023_fabind_68041,
  title = {{FABind: Fast and Accurate Protein-Ligand Binding}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/71739},
}

@inproceedings{neurips2024_flexsbdd_70416,
  title = {{FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/96689},
}

@inproceedings{icml2025_predicting_46644,
  title = {{Predicting mutational effects on protein binding from folding energy}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45926},
}

@inproceedings{neurips2024_deltadock_73096,
  title = {{DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94333},
}

@inproceedings{neurips2025_cpsea_75841,
  title = {{CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=CfOsKx3jF8},
}

@inproceedings{aaai2025_hemenet_9415,
  title = {{HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multi-task Learning}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/32000},
}

@inproceedings{neurips2024_flexmol_74105,
  title = {{FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/97484},
}

@inproceedings{neurips2025_unizyme_75230,
  title = {{UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=5cgm5dV5hr},
}

@inproceedings{iclr2025_mofflow_82809,
  title = {{MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/28990},
}

@inproceedings{iclr2025_sagephos_83036,
  title = {{SAGEPhos: Sage Bio-Coupled and Augmented Fusion for Phosphorylation Site Detection}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/28768},
}

@inproceedings{aaai2026_s_99876,
  title = {{S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/36997},
}

@inproceedings{aaai2026_sculptdrug_100088,
  title = {{SculptDrug: A Spatial Condition-Aware Bayesian Flow Model for Structure-based Drug Design}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/37139},
}

@inproceedings{icml2025_a_47424,
  title = {{A Physics-Augmented Deep Learning Framework for Classifying Single Molecule Force Spectroscopy Data}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45169},
}