mlsanityData to 7 Oct 2026

Autoregressive fragment-based diffusion for pocket-aware ligand design

arXiv 2401.05370 ↗First posted 15 Dec 2023q-bio.BM cs.AI cs.LGcited by 7

On the map: Diffusion models → Flow matching, time series and science

Abstract (arXiv)

In this work, we introduce AutoFragDiff, a fragment-based autoregressive diffusion model for generating 3D molecular structures conditioned on target protein structures. We employ geometric vector perceptrons to predict atom types and spatial coordinates of new molecular fragments conditioned on molecular scaffolds and protein pockets. Our approach improves the local geometry of the resulting 3D molecules while maintaining high predicted binding affinity to protein targets. The model can also perform scaffold extension from user-provided starting molecular scaffold.

Key facts. Cited by 7 papers in the map (data through 7 Oct 2026). Placed in Flow matching, time series and science, one of 14 directions in Diffusion models. Builds on 19 of its 30 references that are in the map. First posted on arXiv 15 Dec 2023.

Builds on

19 of 30 references.

Closest ancestors · 4

Same direction, newest first

  1. 2022Structure-based Drug Design with Equivariant Diffusion Models24 Oct
  2. 2022Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design11 Oct
  3. 2022Equivariant Diffusion for Molecule Generation in 3D31 Mar
  4. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation6 Mar

Other references · 15

  1. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  2. 2022Classifier-Free Diffusion Guidancecited by 5,717
  3. 2016Layer Normalizationcited by 5,579
  4. 2021Variational Diffusion Modelscited by 1,145
  5. 2016Geometric deep learning: going beyond Euclidean datacited by 1,042
  6. 2021E(n) Equivariant Graph Neural Networkscited by 951
  7. 2020Learning from Protein Structure with Geometric Vector Perceptronscited by 308
  8. 2021Autoregressive Diffusion Modelscited by 208
  9. 2022Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pocketscited by 182
  10. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Predictioncited by 176
  11. 2021Geometric Deep Learning on Molecular Representationscited by 113
  12. 2022Generating 3D Molecules for Target Protein Bindingcited by 104
3 more
  1. 2016Protein-Ligand Scoring with Convolutional Neural Networkscited by 57
  2. 2021Learning to design drug-like molecules in three-dimensional space using deep generative modelscited by 37
  3. 2021Structure-aware generation of drug-like moleculescited by 7

Built on by

Cited by year

Citing papers per year: 2024: 3; 2025: 4.

7 papers.

  1. 2024Diffusion Models in textitDe Novo Drug Designcited by 26
  2. 2024TAGMol: Target-Aware Gradient-guided Molecule Generationcited by 12
  3. 2025Compositional Flows for 3D Molecule and Synthesis Pathway Co-designcited by 6
  4. 2024NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Librariescited by 3
  5. 2025Unraveling the Potential of Diffusion Models in Small Molecule Generationcited by 3
  6. 2025HybridLinker: Topology-Guided Posterior Sampling for Enhanced Diversity and Validity in 3D Molecular Linker Generationcited by 2
  7. 2025FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity predictioncited by 2

Similar, not cited

Close in wording, no citation either way

  1. 2024AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design
  2. 2023Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration
  3. 2025MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation
  4. 2022DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
  5. 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D
  6. 2025A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
  7. 2026Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimization
  8. 2026Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints