mlsanityData to 14 Oct 2026

MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space

arXiv 2404.12141 ↗First posted 18 Apr 2024q-bio.BM cs.LGcited by 48

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Abstract (arXiv)

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Key facts. Cited by 48 papers in the map (data through 14 Oct 2026). Builds on 19 of its 38 references that are in the map. First posted on arXiv 18 Apr 2024.

Builds on

19 of 38 references.

References · 19

  1. 2020Denoising Diffusion Probabilistic Modelscited by 21,076
  2. 2016Layer Normalizationcited by 5,669
  3. 2021E(n) Equivariant Graph Neural Networkscited by 965
  4. 2016Automatic chemical design using a data-driven continuous representation of moleculescited by 765
  5. 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 677
  6. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generationcited by 516
  7. 2022Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pocketscited by 183
  8. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Predictioncited by 177
  9. 2022A 3D Generative Model for Structure-Based Drug Designcited by 149
  10. 2022Generating 3D Molecules for Target Protein Bindingcited by 104
  11. 2024DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Designcited by 88
  12. 2023MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generationcited by 65
7 more
  1. 2023Bayesian Flow Networkscited by 63
  2. 2023Equivariant Flow Matching with Hybrid Probability Transportcited by 60
  3. 2022Structure-based drug design with geometric deep learningcited by 40
  4. 2017Molecular Generation with Recurrent Neural Networks (RNNs)cited by 36
  5. 2020Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Modelscited by 33
  6. 2022Zero-Shot 3D Drug Design by Sketching and Generatingcited by 24
  7. 2024Unified Generative Modeling of 3D Molecules via Bayesian Flow Networkscited by 18

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2024: 8; 2025: 27; 2026: 13.

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  1. 2025PharmAgents: Building a Virtual Pharma with Large Language Model Agentscited by 21
  2. 2024Generative Flows on Synthetic Pathway for Drug Designcited by 20
  3. 2024CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graphcited by 19
  4. 2024Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks?cited by 18
  5. 2025A Periodic Bayesian Flow for Material Generationcited by 16
  6. 2025Flow Matching Meets Biology and Life Science: A Surveycited by 14
  7. 2025UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Designcited by 12
  8. 2025Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modelingcited by 11
  9. 2024Advancing biomolecular understanding and design following human instructionscited by 10
  10. 2024Decomposed Direct Preference Optimization for Structure-Based Drug Designcited by 7
  11. 2024Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networkscited by 6
  12. 2025Compositional Flows for 3D Molecule and Synthesis Pathway Co-designcited by 6
36 more
  1. 2025Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedulecited by 6
  2. 2025Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Numbercited by 6
  3. 2025FROGENT: An End-to-End Full-process Drug Design Multi-Agent Systemcited by 4
  4. 2025Manipulating 3D Molecules in a Fixed-Dimensional E(3)-Equivariant Latent Spacecited by 3
  5. 2025FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity predictioncited by 3
  6. 2025Unified all-atom molecule generation with neural fieldscited by 3
  7. 2025Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flowscited by 2
  8. 2025Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integrationcited by 2
  9. 2025MolChord: Structure-Sequence Alignment for Protein-Guided Drug Designcited by 2
  10. 2026CAGenMol: Condition-Aware Diffusion Language Model for Goal-Directed Molecular Generationcited by 2
  11. 2024From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metricscited by 1
  12. 2025AMix-1: A Pathway to Test-Time Scalable Protein Foundation Modelcited by 1
  13. 2025MolPIF: A Parameter Interpolation Flow Model for Molecule Generationcited by 1
  14. 2025IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Datacited by 1
  15. 2025Transport-Coupled Bayesian Flows for Molecular Graph Generationcited by 1
  16. 2025Full-Atom Peptide Design via Riemannian-Euclidean Bayesian Flow Networkscited by 1
  17. 2026Variational Bayesian Flow Network for Graph Generationcited by 1
  18. 2026ConfHit: Conformal Generative Design with Oracle Free Guaranteescited by 1
  19. 2026MolSafeEval: A Benchmark for Uncovering Safety Risks in AI-Generated Moleculescited by 1
  20. 2024Sampling Out-of-Distribution Chemical Spaces via Bayesian Flowcited by 0
  21. 2025TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Designcited by 0
  22. 2025PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generationcited by 0
  23. 2025Assay2Mol: large language model-based drug design using BioAssay contextcited by 0
  24. 2025MolMark: Safeguarding Molecular Structures through Learnable Atom-Level Watermarkingcited by 0
  25. 2025MSCoD: An Enhanced Bayesian Updating Framework with Multi-Scale Information Bottleneck and Cooperative Attention for Structure-Based Drug Designcited by 0
  26. 2025SiDGen: Structure-informed Diffusion for Generative modeling of Ligands for Proteinscited by 0
  27. 2025SculptDrug : A Spatial Condition-Aware Bayesian Flow Model for Structure-based Drug Designcited by 0
  28. 2026EvoEGF-Mol: Evolving Exponential Geodesic Flow for Structure-based Drug Designcited by 0
  29. 2026Routing by Reaching: Composition of Pre-trained GFlowNets for Multi-Objective Generationcited by 0
  30. 2026From Holo Pockets to Electron Density: GPT-style Drug Design with Densitycited by 0
  31. 2026Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimizationcited by 0
  32. 2026Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Designcited by 0
  33. 2026Fine-Tuning Diffusion Models for Molecular Generation via Reinforcement Learning and Fast Samplingcited by 0
  34. 2026Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Couplingcited by 0
  35. 2026Fused Bayesian Flow Networks for Dual-Target Molecular Designcited by 0
  36. 2026A Systematic Evaluation of Molecule Generation Models for De Novo Drug Design: From Benchmarks to Practical Insightscited by 0