% Key papers for Structure-based 3D molecule generation (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{iclr2023_diffdock_33073,
  title = {{DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/11750},
}

@inproceedings{icml2020_multi_38473,
  title = {{Multi-Objective Molecule Generation using Interpretable Substructures}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2020},
  url = {https://icml.cc/virtual/2020/poster/6214},
}

@inproceedings{neurips2020_cogmol_59543,
  title = {{CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2020},
  url = {https://nips.cc/virtual/2020/poster/18994},
}

@inproceedings{icml2022_pocket2mol_41016,
  title = {{Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/17849},
}

@inproceedings{neurips2019_a_57821,
  title = {{A Model to Search for Synthesizable Molecules}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2019},
  url = {https://nips.cc/virtual/2019/poster/13870},
}

@inproceedings{icml2019_molecular_37549,
  title = {{Molecular Hypergraph Grammar with Its Application to Molecular Optimization}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2019},
  url = {https://icml.cc/virtual/2019/poster/3670},
}

@inproceedings{icml2022_generating_40622,
  title = {{Generating 3D Molecules for Target Protein Binding}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/16435},
}

@inproceedings{aaai2020_core_100231,
  title = {{CORE: Automatic Molecule Optimization Using Copy \& Refine Strategy}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2020},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/5404},
}

@inproceedings{iclr2022_learning_31413,
  title = {{Learning to Extend Molecular Scaffolds with Structural Motifs}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2022},
  url = {https://iclr.cc/virtual/2022/poster/7209},
}

@inproceedings{neurips2020_guiding_59980,
  title = {{Guiding Deep Molecular Optimization with Genetic Exploration}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2020},
  url = {https://nips.cc/virtual/2020/poster/17800},
}

@inproceedings{iclr2021_mars_30580,
  title = {{MARS: Markov Molecular Sampling for Multi-objective Drug Discovery}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2021},
  url = {https://iclr.cc/virtual/2021/poster/3352},
}

@inproceedings{neurips2022_reinforced_64918,
  title = {{Reinforced Genetic Algorithm for Structure-based Drug Design}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/54077},
}

@inproceedings{neurips2023_tartarus_69109,
  title = {{Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/73501},
}

@inproceedings{iclr2022_amortized_31068,
  title = {{Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2022},
  url = {https://iclr.cc/virtual/2022/poster/6883},
}

@inproceedings{icml2022_limo_40735,
  title = {{LIMO: Latent Inceptionism for Targeted Molecule Generation}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/16741},
}

@inproceedings{neurips2021_atom3d_61752,
  title = {{ATOM3D: Tasks on Molecules in Three Dimensions}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2021},
  url = {https://openreview.net/forum?id=FkDZLpK1Ml2},
}

@inproceedings{aaai2023_retrosynthesis_4526,
  title = {{Retrosynthesis Prediction with Local Template Retrieval}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2023},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/25664},
}

@inproceedings{neurips2023_prefix_67909,
  title = {{Prefix-Tree Decoding for Predicting Mass Spectra from Molecules}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/71858},
}

@inproceedings{aaai2024_gxvaes_6168,
  title = {{GxVAEs: Two Joint VAEs Generate Hit Molecules from Gene Expression Profiles}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/29248},
}

@inproceedings{iclr2025_synflownet_83874,
  title = {{SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/27946},
}

@inproceedings{icml2024_molcraft_44116,
  title = {{MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34336},
}

@inproceedings{neurips2024_rgfn_73419,
  title = {{RGFN: Synthesizable Molecular Generation Using GFlowNets}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94040},
}

@inproceedings{icml2024_projecting_45549,
  title = {{Projecting Molecules into Synthesizable Chemical Spaces}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/32903},
}

@inproceedings{iclr2025_shepherd_81722,
  title = {{ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/30057},
}

@inproceedings{neurips2024_aligning_71204,
  title = {{Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/96029},
}

@inproceedings{iclr2025_generative_83503,
  title = {{Generative Flows on Synthetic Pathway for Drug Design}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/28313},
}

@inproceedings{iclr2024_retrobridge_33700,
  title = {{RetroBridge: Modeling Retrosynthesis with Markov Bridges}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19375},
}

@inproceedings{icml2024_structure_44095,
  title = {{Structure-based drug design by denoising voxel grids}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34357},
}

@inproceedings{neurips2024_uniif_73036,
  title = {{UniIF: Unified Molecule Inverse Folding}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94387},
}

@inproceedings{iclr2025_structure_82000,
  title = {{Structure Language Models for Protein Conformation Generation}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/29785},
}

@inproceedings{iclr2025_cbgbench_83346,
  title = {{CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/28468},
}

@inproceedings{iclr2024_removing_33715,
  title = {{Removing Biases from Molecular Representations via Information Maximization}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19360},
}

@inproceedings{icml2025_empower_46496,
  title = {{Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/46071},
}

@inproceedings{neurips2025_controllable_78162,
  title = {{Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=biM1m6VXSD},
}

@inproceedings{iclr2025_madgen_80922,
  title = {{MADGEN: Mass-Spec attends to De Novo Molecular generation}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2025},
  url = {https://iclr.cc/virtual/2025/poster/30846},
}

@inproceedings{icml2025_mf_46032,
  title = {{MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/46515},
}

@inproceedings{neurips2024_turbohopp_73643,
  title = {{TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/93849},
}

@inproceedings{neurips2025_oligogym_76039,
  title = {{OligoGym: Curated Datasets and Benchmarks for Oligonucleotide Drug Discovery}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=EtQ2YAWHYs},
}