mlsanityData to 7 Oct 2026

Zero-Shot 3D Drug Design by Sketching and Generating

arXiv 2209.13865 ↗First posted 28 Sep 2022cs.CE q-bio.BMcited by 24

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Abstract (arXiv)

Drug design is a crucial step in the drug discovery cycle. Recently, various deep learning-based methods design drugs by generating novel molecules from scratch, avoiding traversing large-scale drug libraries. However, they depend on scarce experimental data or time-consuming docking simulation, leading to overfitting issues with limited training data and slow generation speed. In this study, we propose the zero-shot drug design method DESERT (Drug dEsign by SkEtching and geneRaTing). Specifically, DESERT splits the design process into two stages: sketching and generating, and bridges them with the molecular shape. The two-stage fashion enables our method to utilize the large-scale molecular database to reduce the need for experimental data and docking simulation. Experiments show that DESERT achieves a new state-of-the-art at a fast speed.

Key facts. Cited by 24 papers in the map (data through 7 Oct 2026). First posted on arXiv 28 Sep 2022.

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2023: 7; 2024: 8; 2025: 8; 2026: 1.

24 papers.

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  1. 2024DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Designcited by 87
  2. 2024MolCRAFT: Structure-Based Drug Design in Continuous Parameter Spacecited by 48
  3. 20233D molecule generation by denoising voxel gridscited by 38
  4. 2024A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applicationscited by 28
  5. 2024DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimizationcited by 27
  6. 2023Learning Subpocket Prototypes for Generalizable Structure-based Drug Designcited by 25
  7. 2024Structure-based drug design by denoising voxel gridscited by 18
  8. 2024TAGMol: Target-Aware Gradient-guided Molecule Generationcited by 12
  9. 2025Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidancecited by 10
  10. 2024Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusioncited by 9
  11. 2023Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Modelscited by 7
  12. 2025Unified Guidance for Geometry-Conditioned Molecular Generationcited by 7
12 more
  1. 2023PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modelingcited by 4
  2. 20253DMolFormer: A Dual-channel Framework for Structure-based Drug Discoverycited by 4
  3. 20233D Molecular Generation via Virtual Dynamicscited by 3
  4. 2023Geometric Deep Learning for Structure-Based Drug Design: A Surveycited by 2
  5. 2025MolChord: Structure-Sequence Alignment for Protein-Guided Drug Designcited by 2
  6. 2025Unified all-atom molecule generation with neural fieldscited by 2
  7. 2026CAGenMol: Condition-Aware Diffusion Language Model for Goal-Directed Molecular Generationcited by 2
  8. 2024Structure-Based Drug Design via 3D Molecular Generative Pre-training and Samplingcited by 1
  9. 2025ProtPainter: Draw or Drag Protein via Topology-guided Diffusioncited by 1
  10. 2023Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methodscited by 0
  11. 2025TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Designcited by 0
  12. 2025MSCoD: An Enhanced Bayesian Updating Framework with Multi-Scale Information Bottleneck and Cooperative Attention for Structure-Based Drug Designcited by 0