mlsanityData to 14 Oct 2026

FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation

arXiv 2504.10564 ↗First posted 14 Apr 2025q-bio.QM cs.LG q-bio.BMcited by 18

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Abstract (arXiv)

We introduce FLOWR, a novel structure-based framework for the generation and optimization of three-dimensional ligands. FLOWR integrates continuous and categorical flow matching with equivariant optimal transport, enhanced by an efficient protein pocket conditioning. Alongside FLOWR, we present SPINDR, a thoroughly curated dataset comprising ligand-pocket co-crystal complexes specifically designed to address existing data quality issues. Empirical evaluations demonstrate that FLOWR surpasses current state-of-the-art diffusion- and flow-based methods in terms of PoseBusters-validity, pose accuracy, and interaction recovery, while offering a significant inference speedup, achieving up to 70-fold faster performance. In addition, we introduce FLOWR:multi, a highly accurate multi-purpose model allowing for the targeted sampling of novel ligands that adhere to predefined interaction profiles and chemical substructures for fragment-based design without the need of re-training or any re-sampling strategies

Key facts. Cited by 18 papers in the map (data through 14 Oct 2026). Builds on 20 of its 60 references that are in the map. First posted on arXiv 14 Apr 2025.

Builds on

20 of 60 references.

References · 20

  1. 2022Flow Matching for Generative Modelingcited by 5,702
  2. 2022Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flowcited by 3,700
  3. 2022RePaint: Inpainting using Denoising Diffusion Probabilistic Modelscited by 1,430
  4. 2022Building Normalizing Flows with Stochastic Interpolantscited by 995
  5. 2023Improving and generalizing flow-based generative models with minibatch optimal transportcited by 879
  6. 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 677
  7. 2022Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioningcited by 373
  8. 2024Discrete Flow Matchingcited by 317
  9. 2024Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Designcited by 305
  10. 2022Structure-based Drug Design with Equivariant Diffusion Modelscited by 217
  11. 2022Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pocketscited by 183
  12. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Predictioncited by 177
8 more
  1. 2022A 3D Generative Model for Structure-Based Drug Designcited by 149
  2. 2023Equivariant flow matchingcited by 135
  3. 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generationcited by 98
  4. 2024Flow Matching with General Discrete Paths: A Kinetic-Optimal Perspectivecited by 57
  5. 2023Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generationcited by 50
  6. 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matchingcited by 41
  7. 2024PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance samplingcited by 19
  8. 2024Assessing interaction recovery of predicted protein-ligand posescited by 3

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 10; 2026: 8.

18 papers.

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  1. 2025FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generationcited by 21
  2. 2025Flow Matching Meets Biology and Life Science: A Surveycited by 14
  3. 2025Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamicscited by 11
  4. 2025FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity predictioncited by 3
  5. 2025Predictive Feature Caching for Training-free Acceleration of Molecular Geometry Generationcited by 2
  6. 2025MolPIF: A Parameter Interpolation Flow Model for Molecule Generationcited by 1
  7. 2026From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistrycited by 1
  8. 2026Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimizationcited by 1
  9. 2025Assay2Mol: large language model-based drug design using BioAssay contextcited by 0
  10. 2025Flow-Based Fragment Identification via Binding Site-Specific Latent Representationscited by 0
  11. 2025Discovery of Sustainable Refrigerants through Physics-Informed RL Fine-Tuning of Sequence Modelscited by 0
  12. 2025OMTRA: A Multi-Task Generative Model for Structure-Based Drug Designcited by 0
6 more
  1. 2026EvoEGF-Mol: Evolving Exponential Geodesic Flow for Structure-based Drug Designcited by 0
  2. 2026Sesame: Structure-Aware Molecular Generation via Spatial Density-Map Conditioningcited by 0
  3. 2026SynLaD: Latent Diffusion for Generating Synthesizable Molecules Conditioned on 3D Pharmacophore Profilescited by 0
  4. 2026CORAL: Learning Amyloid Fibril Ligand Docking with Cooperative Binding Rewardscited by 0
  5. 2026DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Modelscited by 0
  6. 2026Ensemble-Conditioned Molecular Designcited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2024FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
  2. 2023Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design
  3. 2025FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble
  4. 2025Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Number
  5. 2025Energy-Based Flow Matching for Generating 3D Molecular Structure
  6. 20253DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery
  7. 2026Generating Cyclic Conformers with Flow Matching in Cremer-Pople Coordinates
  8. 2024Exploring Discrete Flow Matching for 3D De Novo Molecule Generation