mlsanityData to 14 Oct 2026

Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule

arXiv 2505.07286 ↗First posted 12 May 2025q-bio.BM cs.AI cs.LGcited by 6

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Abstract (arXiv)

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Key facts. Cited by 6 papers in the map (data through 14 Oct 2026). Builds on 16 of its 33 references that are in the map. First posted on arXiv 12 May 2025.

Builds on

16 of 33 references.

References · 16

  1. 2021Variational Diffusion Modelscited by 1,153
  2. 2022DiffDock: Diffusion Steps, Twists, and Turns for Molecular Dockingcited by 313
  3. 2024Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Designcited by 305
  4. 2022Continuous diffusion for categorical datacited by 214
  5. 2022Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pocketscited by 183
  6. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Predictioncited by 177
  7. 2022A 3D Generative Model for Structure-Based Drug Designcited by 149
  8. 2022Generating 3D Molecules for Target Protein Bindingcited by 104
  9. 2024DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Designcited by 88
  10. 2023MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generationcited by 65
  11. 2023Bayesian Flow Networkscited by 63
  12. 2023Equivariant Flow Matching with Hybrid Probability Transportcited by 60
4 more
  1. 2024MolCRAFT: Structure-Based Drug Design in Continuous Parameter Spacecited by 48
  2. 2022Structure-based drug design with geometric deep learningcited by 40
  3. 2023Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaborationcited by 30
  4. 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: 2025: 3; 2026: 3.

6 papers.

  1. 2025Kinetic Langevin Diffusion for Crystalline Materials Generationcited by 9
  2. 2025MolPIF: A Parameter Interpolation Flow Model for Molecule Generationcited by 1
  3. 2025SiDGen: Structure-informed Diffusion for Generative modeling of Ligands for Proteinscited by 0
  4. 2026EvoEGF-Mol: Evolving Exponential Geodesic Flow for Structure-based Drug Designcited by 0
  5. 2026Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Designcited by 0
  6. 2026Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Couplingcited by 0