mlsanityData to 14 Oct 2026

Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models

arXiv 2110.15200 ↗First posted 28 Oct 2021q-bio.QM cs.LGcited by 73

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Cited by 24 in Diffusion models, but placed by its own abstract, which didn’t fit.

Abstract (arXiv)

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to generating 3D molecules predicted to bind to proteins by sampling the conditional distribution of protein-ligand binding interactions. In this work, we describe for the first time a deep learning system for generating 3D molecular structures conditioned on a receptor binding site. We approach the problem using a conditional variational autoencoder trained on an atomic density grid representation of cross-docked protein-ligand structures. We apply atom fitting and bond inference procedures to construct valid molecular conformations from generated atomic densities. We evaluate the properties of the generated molecules and demonstrate that they change significantly when conditioned on mutated receptors. We also explore the latent space learned by our generative model using sampling and interpolation techniques. This work opens the door for end-to-end prediction of stable bioactive molecules from protein structures with deep learning.

Key facts. Cited by 73 papers in the map (data through 14 Oct 2026). Builds on 1 of its 8 references that are in the map. First posted on arXiv 28 Oct 2021.

Builds on

1 of 8 references.

References · 1

  1. 2015U-Net: Convolutional Networks for Biomedical Image Segmentationcited by 19,713

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2022: 7; 2023: 15; 2024: 19; 2025: 25; 2026: 7.

73 papers.

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  1. 2022Structure-based Drug Design with Equivariant Diffusion Modelscited by 217
  2. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Predictioncited by 177
  3. 2022Generating 3D Molecules for Target Protein Bindingcited by 104
  4. 2024DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Designcited by 88
  5. 2023A Comprehensive Survey on Deep Graph Representation Learningcited by 72
  6. 2024Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generationcited by 54
  7. 20233D molecule generation by denoising voxel gridscited by 40
  8. 2024DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimizationcited by 27
  9. 2023Learning Subpocket Prototypes for Generalizable Structure-based Drug Designcited by 25
  10. 2024Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimizationcited by 25
  11. 2022Graph Neural Networks for Moleculescited by 21
  12. 2024Generative Flows on Synthetic Pathway for Drug Designcited by 20
38 more
  1. 2022Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Designcited by 19
  2. 2024Structure-based drug design by denoising voxel gridscited by 19
  3. 2025Multi-domain Distribution Learning for De Novo Drug Designcited by 15
  4. 2023Generation of 3D Molecules in Pockets via Language Modelcited by 13
  5. 2025Equivariant Neural Diffusion for Molecule Generationcited by 13
  6. 2024TAGMol: Target-Aware Gradient-guided Molecule Generationcited by 12
  7. 2023DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraintscited by 10
  8. 2023An Equivariant Generative Framework for Molecular Graph-Structure Co-Designcited by 10
  9. 2025Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidancecited by 10
  10. 2025ELECTRA: A Cartesian Network for 3D Charge Density Prediction with Floating Orbitalscited by 10
  11. 2023SILVR: Guided Diffusion for Molecule Generationcited by 9
  12. 2023PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embeddingcited by 7
  13. 2024Decomposed Direct Preference Optimization for Structure-Based Drug Designcited by 7
  14. 2025Compositional Flows for 3D Molecule and Synthesis Pathway Co-designcited by 6
  15. 2025Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Numbercited by 6
  16. 2024General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Designcited by 5
  17. 2024Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Predictioncited by 5
  18. 2023PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modelingcited by 4
  19. 20253DMolFormer: A Dual-channel Framework for Structure-based Drug Discoverycited by 4
  20. 2022Structure-based drug discovery with deep learningcited by 3
  21. 20233D Molecular Generation via Virtual Dynamicscited by 3
  22. 2024Guided Multi-objective Generative AI to Enhance Structure-based Drug Designcited by 3
  23. 2024TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Modelscited by 3
  24. 2024Rectified Flow For Structure Based Drug Designcited by 3
  25. 2025BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generationcited by 3
  26. 2025Unified all-atom molecule generation with neural fieldscited by 3
  27. 2023Geometric Deep Learning for Structure-Based Drug Design: A Surveycited by 2
  28. 2023TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Designcited by 2
  29. 2023Docking-based generative approaches in the search for new drug candidatescited by 2
  30. 2025Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flowscited by 2
  31. 2025Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integrationcited by 2
  32. 2025MolChord: Structure-Sequence Alignment for Protein-Guided Drug Designcited by 2
  33. 2026Global Plane Waves From Local Gaussians: Periodic Charge Densities in a Blinkcited by 2
  34. 2022Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generationcited by 1
  35. 2024Response Matching for generating materials and moleculescited by 1
  36. 2024From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metricscited by 1
  37. 2024Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Designcited by 1
  38. 2024Bridging the Gap between Learning and Inference for Diffusion-Based Molecule Generationcited by 1

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