mlsanityData to 7 Oct 2026

AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies

arXiv 2308.05027 ↗First posted 28 Jul 2023q-bio.BM cs.LG stat.MLcited by 35

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

Abstract (arXiv)

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion priors to improve the denoising process. Our approach improves protein diffusion by taking advantage of domain knowledge and physics-based constraints; handles sequence-length changes; and reduces memory complexity by an order of magnitude, enabling backbone and side chain generation. We validate AbDiffuser in silico and in vitro. Numerical experiments showcase the ability of AbDiffuser to generate antibodies that closely track the sequence and structural properties of a reference set. Laboratory experiments confirm that all 16 HER2 antibodies discovered were expressed at high levels and that 57.1% of the selected designs were tight binders.

Key facts. Cited by 35 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 38 of its 102 references that are in the map. First posted on arXiv 28 Jul 2023.

Builds on

38 of 102 references.

Closest ancestors · 8

Same direction, newest first

  1. 2023DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models8 Apr
  2. 2023EigenFold: Generative Protein Structure Prediction with Diffusion Models5 Apr
  3. 2023SE(3) diffusion model with application to protein backbone generation5 Feb
  4. 2022Diffusion Models for Graphs Benefit From Discrete State Spaces4 Oct
  5. 2022Protein structure generation via folding diffusion30 Sep
  6. 2022DiGress: Discrete Denoising diffusion for graph generation29 Sep
  7. 2022Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem8 Jun
  8. 2022Equivariant Diffusion for Molecule Generation in 3D31 Mar

Other references · 30

  1. 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,204
  2. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  3. 2019PyTorch: An Imperative Style, High-Performance Deep Learning Librarycited by 20,160
  4. 2015Deep Unsupervised Learning using Nonequilibrium Thermodynamicscited by 7,005
  5. 2018How Powerful are Graph Neural Networks?cited by 4,355
  6. 2021Improved Denoising Diffusion Probabilistic Modelscited by 3,736
  7. 2016Gaussian Error Linear Units (GELUs)cited by 3,431
  8. 2021Structured Denoising Diffusion Models in Discrete State-Spacescited by 1,665
  9. 2021MLP-Mixer: An all-MLP Architecture for Visioncited by 1,441
  10. 2021Variational Diffusion Modelscited by 1,145
  11. 2021E(n) Equivariant Graph Neural Networkscited by 951
  12. 2019Efficient Graph Generation with Graph Recurrent Attention Networkscited by 231
18 more
  1. 2022Riemannian Score-Based Generative Modellingcited by 216
  2. 2021Frame Averaging for Invariant and Equivariant Network Designcited by 166
  3. 2020ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computingcited by 162
  4. 2016How to learn a graph from smooth signalscited by 146
  5. 2017Universal Function Approximation by Deep Neural Nets with Bounded Width and ReLU Activationscited by 104
  6. 2022Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoderscited by 99
  7. 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generatorscited by 96
  8. 2021Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-designcited by 82
  9. 2022Conditional Antibody Design as 3D Equivariant Graph Translationcited by 75
  10. 2021Unleashing Transformers: Parallel Token Prediction with Discrete Absorbing Diffusion for Fast High-Resolution Image Generation from Vector-Quantized Codescited by 71
  11. 2022Equivariant Graph Mechanics Networks with Constraintscited by 67
  12. 2023Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Cloudscited by 53
  13. 2021Deciphering antibody affinity maturation with language models and weakly supervised learningcited by 52
  14. 2023End-to-End Full-Atom Antibody Designcited by 48
  15. 2022Protein Sequence and Structure Co-Design with Equivariant Translationcited by 31
  16. 2023Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equationcited by 18
  17. 2022PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence designcited by 8
  18. 2022Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-designcited by 3

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2023: 2; 2024: 16; 2025: 12; 2026: 5.

35 papers.

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By area:

  1. 2025All-atom Diffusion Transformers: Unified generative modelling of molecules and materialscited by 75
  2. 2023A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systemscited by 65
  3. 2024Protein Conformation Generation via Force-Guided SE(3) Diffusion Modelscited by 44
  4. 2024Full-Atom Peptide Design based on Multi-modal Flow Matchingcited by 34
  5. 2024Antigen-Specific Antibody Design via Direct Energy-based Preference Optimizationcited by 30
  6. 2023Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Designcited by 29
  7. 2024A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applicationscited by 28
  8. 2024A Canonicalization Perspective on Invariant and Equivariant Learningcited by 25
  9. 2024Physics-Regularized Multi-Modal Image Assimilation for Brain Tumor Localizationcited by 9
  10. 2024Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimizationcited by 9
  11. 2024Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extensioncited by 9
  12. 2025An All-Atom Generative Model for Designing Protein Complexescited by 9
23 more
  1. 2025Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Bindingcited by 9
  2. 2024Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimizationcited by 8
  3. 2024Improving Antibody Design with Force-Guided Sampling in Diffusion Modelscited by 7
  4. 2025AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusioncited by 4
  5. 2025AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Designcited by 4
  6. 2026CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Designcited by 4
  7. 2024Structure Preserving Diffusion Modelscited by 3
  8. 2025Guided Sequence-Structure Generative Modeling for Iterative Antibody Optimizationcited by 3
  9. 2026Surface-based Molecular Design with Multi-modal Flow Matchingcited by 3
  10. 2024Diffusion-based Graph Generative Methodscited by 2
  11. 2025Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modelingcited by 2
  12. 2025Unified all-atom molecule generation with neural fieldscited by 2
  13. 2024ADIOS: Antibody Development via Opponent Shapingcited by 1
  14. 2024Recent advances in interpretable machine learning using structure-based protein representationscited by 1
  15. 2025Towards More Accurate Full-Atom Antibody Co-Designcited by 1
  16. 2025Generative Co-Design of Antibody Sequences and Structures via Black-Box Guidance in a Shared Latent Spacecited by 1
  17. 2024Decoupled Sequence and Structure Generation for Realistic Antibody Designcited by 0
  18. 2024Active learning for energy-based antibody optimization and enhanced screeningcited by 0
  19. 2025Latent Retrieval Augmented Generation of Cross-Domain Protein Binderscited by 0
  20. 2025FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equationcited by 0
  21. 2026Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusioncited by 0
  22. 2026ABOPD: Antibody CDR Design via On-Policy Distillationcited by 0
  23. 2026Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Designcited by 0

Similar, not cited

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  1. 2024De novo antibody design with SE(3) diffusion
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  3. 2025Guided Generation for Developable Antibodies
  4. 2025AffinityFlow: Guided Flows for Antibody Affinity Maturation
  5. 2023AntiBARTy Diffusion for Property Guided Antibody Design
  6. 2023Protein Discovery with Discrete Walk-Jump Sampling
  7. 2024Pareto-Optimal Energy Alignment for Designing Nature-Like Antibodies
  8. 2025dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen