# Flexible MOF Generation with Torsion-Aware Flow Matching

arXiv: https://arxiv.org/abs/2505.17914 · HTML: https://mlsanity.com/paper/2505.17914/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 66 references that are in the map.
- First posted on arXiv 23 May 2025.

## Builds on (most cited first, 30 of 32)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Root Mean Square Layer Normalization](https://mlsanity.com/paper/1910.07467/) (2019)
- [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)
- [AllenNLP: A Deep Semantic Natural Language Processing Platform](https://mlsanity.com/paper/1803.07640/) (2018)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [Multisample Flow Matching: Straightening Flows with Minibatch Couplings](https://mlsanity.com/paper/2304.14772/) (2023)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Flow Matching on General Geometries](https://mlsanity.com/paper/2302.03660/) (2023)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [SE(3)-Stochastic Flow Matching for Protein Backbone Generation](https://mlsanity.com/paper/2310.02391/) (2023)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [FlowMM: Generating Materials with Riemannian Flow Matching](https://mlsanity.com/paper/2406.04713/) (2024)
- [An Analysis of SVD for Deep Rotation Estimation](https://mlsanity.com/paper/2006.14616/) (2020)
- [All-atom Diffusion Transformers: Unified generative modelling of molecules and materials](https://mlsanity.com/paper/2503.03965/) (2025)
- [Space Group Constrained Crystal Generation](https://mlsanity.com/paper/2402.03992/) (2024)
- [Deep Regression on Manifolds: A 3D Rotation Case Study](https://mlsanity.com/paper/2103.16317/) (2021)
- [Orb: A Fast, Scalable Neural Network Potential](https://mlsanity.com/paper/2410.22570/) (2024)
- [Proteina: Scaling Flow-based Protein Structure Generative Models](https://mlsanity.com/paper/2503.00710/) (2025)
- [Equivariant Flow Matching with Hybrid Probability Transport](https://mlsanity.com/paper/2312.07168/) (2023)
- [Swallowing the Bitter Pill: Simplified Scalable Conformer Generation](https://mlsanity.com/paper/2311.17932/) (2023)
- [Improved motif-scaffolding with SE(3) flow matching](https://mlsanity.com/paper/2401.04082/) (2024)
- [Learning with 3D rotations, a hitchhiker's guide to SO(3)](https://mlsanity.com/paper/2404.11735/) (2024)
- [DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing](https://mlsanity.com/paper/2306.01794/) (2023)

## Built on by (most cited first, 10 of 10)

- [Multimodal Crystal Flow: Any-to-Any Modality Generation for Unified Crystal Modeling](https://mlsanity.com/paper/2602.20210/) (2026)
- [The Rise of Generative AI for Metal-Organic Framework Design and Synthesis](https://mlsanity.com/paper/2508.13197/) (2025)
- [Mofasa: A Step Change in Metal-Organic Framework Generation](https://mlsanity.com/paper/2512.01756/) (2025)
- [MolCrystalFlow: Molecular Crystal Structure Prediction via Flow Matching](https://mlsanity.com/paper/2602.16020/) (2026)
- [Speaking the Language of Science: Toward a General-Purpose Generative Foundation Model for the Natural Sciences](https://mlsanity.com/paper/2606.16905/) (2026)
- [Enhancing Spatial Reasoning in Large Language Models for Metal-Organic Frameworks Structure Prediction](https://mlsanity.com/paper/2601.09285/) (2026)
- [Packora: Systematic Design for Generative Molecular Crystal Structure Prediction](https://mlsanity.com/paper/2608.26962/) (2026)
- [GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generation](https://mlsanity.com/paper/2609.37158/) (2026)
- [Riemannian Flow Models with Reinforcement Learning for Molecular Crystal Structure Prediction](https://mlsanity.com/paper/2609.39773/) (2026)
- [AnchorPose for Geometry-Aware MOF Assembly through Meso-Grained Pose Generation](https://mlsanity.com/paper/2610.05843/) (2026)

## Abstract (arXiv)

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.