# Multi-domain Distribution Learning for De Novo Drug Design

arXiv: https://arxiv.org/abs/2508.17815 · HTML: https://mlsanity.com/paper/2508.17815/

## Key facts

- Cited by 15 papers in the map (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 45 of its 77 references that are in the map.
- First posted on arXiv 25 Aug 2025.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 45)

- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Diffusion Model Alignment Using Direct Preference Optimization](https://mlsanity.com/paper/2311.12908/) (2023)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning](https://mlsanity.com/paper/2208.04202/) (2022)
- [Learning from Protein Structure with Geometric Vector Perceptrons](https://mlsanity.com/paper/2009.01411/) (2020)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [Optimization of Molecules via Deep Reinforcement Learning](https://mlsanity.com/paper/1810.08678/) (2018)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets](https://mlsanity.com/paper/2205.07249/) (2022)
- [3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction](https://mlsanity.com/paper/2303.03543/) (2023)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [E(n) Equivariant Normalizing Flows](https://mlsanity.com/paper/2105.09016/) (2021)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [A 3D Generative Model for Structure-Based Drug Design](https://mlsanity.com/paper/2203.10446/) (2022)
- [Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design](https://mlsanity.com/paper/2210.05274/) (2022)
- [Generating 3D Molecules for Target Protein Binding](https://mlsanity.com/paper/2204.09410/) (2022)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)
- [DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design](https://mlsanity.com/paper/2403.07902/) (2024)
- [Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models](https://mlsanity.com/paper/2110.15200/) (2021)

## Built on by (most cited first, 15 of 15)

- [Branching Flows: Discrete, Continuous, and Manifold Flow Matching with Splits and Deletions](https://mlsanity.com/paper/2511.09465/) (2025)
- [Mozi: Governed Autonomy for Drug Discovery LLM Agents](https://mlsanity.com/paper/2603.03655/) (2026)
- [MiAD: Mirage Atom Diffusion for De Novo Crystal Generation](https://mlsanity.com/paper/2511.14426/) (2025)
- [FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction](https://mlsanity.com/paper/2510.02578/) (2025)
- [NEAT: Neighborhood-Guided, Efficient, Autoregressive Set Transformer for 3D Molecular Generation](https://mlsanity.com/paper/2512.05844/) (2025)
- [Predictive Feature Caching for Training-free Acceleration of Molecular Geometry Generation](https://mlsanity.com/paper/2510.04646/) (2025)
- [Flow-Based Fragment Identification via Binding Site-Specific Latent Representations](https://mlsanity.com/paper/2509.13216/) (2025)
- [OMTRA: A Multi-Task Generative Model for Structure-Based Drug Design](https://mlsanity.com/paper/2512.05080/) (2025)
- [MacroGuide: Topological Guidance for Macrocycle Generation](https://mlsanity.com/paper/2602.14977/) (2026)
- [Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling](https://mlsanity.com/paper/2606.01628/) (2026)
- [SynLaD: Latent Diffusion for Generating Synthesizable Molecules Conditioned on 3D Pharmacophore Profiles](https://mlsanity.com/paper/2607.01105/) (2026)
- [HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration](https://mlsanity.com/paper/2607.13155/) (2026)
- [CORAL: Learning Amyloid Fibril Ligand Docking with Cooperative Binding Rewards](https://mlsanity.com/paper/2607.17412/) (2026)
- [Language-Informed Flow Matching for Trend-Guided Structure-Based 3D Molecular Generation](https://mlsanity.com/paper/2608.31009/) (2026)
- [Ensemble-Conditioned Molecular Design](https://mlsanity.com/paper/2609.15077/) (2026)

## Abstract (arXiv)

We introduce DrugFlow, a generative model for structure-based drug design that integrates continuous flow matching with discrete Markov bridges, demonstrating state-of-the-art performance in learning chemical, geometric, and physical aspects of three-dimensional protein-ligand data. We endow DrugFlow with an uncertainty estimate that is able to detect out-of-distribution samples. To further enhance the sampling process towards distribution regions with desirable metric values, we propose a joint preference alignment scheme applicable to both flow matching and Markov bridge frameworks. Furthermore, we extend our model to also explore the conformational landscape of the protein by jointly sampling side chain angles and molecules.