# AbFlow : End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matching

arXiv: https://arxiv.org/abs/2602.07084 · HTML: https://mlsanity.com/paper/2602.07084/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 53 references that are in the map.
- First posted on arXiv 6 Feb 2026.

## Builds on (most cited first, 7 of 7)

- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [End-to-End Full-Atom Antibody Design](https://mlsanity.com/paper/2302.00203/) (2023)
- [ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation](https://mlsanity.com/paper/2410.22388/) (2024)
- [EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction](https://mlsanity.com/paper/2302.12177/) (2023)
- [SurfPro: Functional Protein Design Based on Continuous Surface](https://mlsanity.com/paper/2405.06693/) (2024)
- [Accelerating 3D Molecule Generation via Jointly Geometric Optimal Transport](https://mlsanity.com/paper/2405.15252/) (2024)
- [dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen](https://mlsanity.com/paper/2503.01910/) (2025)

## Built on by (most cited first, 2 of 2)

- [ABOPD: Antibody CDR Design via On-Policy Distillation](https://mlsanity.com/paper/2607.18835/) (2026)
- [AbGaze: Attentive Geometric Representation Learning for End-to-End Antibody Design](https://mlsanity.com/paper/2609.35296/) (2026)

## Abstract (arXiv)

Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle to fully exploit antigen-specific geometric information for optimizing local binding interfaces and global structures. To overcome these limitations, we introduce AbFlow, a paratope-restricted one-step flow-matching framework for designing full-atom antibodies end-to-end. AbFlow incorporates an extended velocity field network featuring an equivariant Surface Multi-channel Encoder, which uses surface-level antigen interaction data to refine the antibody structure, particularly the CDR-H3 region. Extensive experiments in paratope-centric antibody design, multi-CDRs and full-atom antibody design, binding affinity optimization, and complex structure prediction show that AbFlow produces superior antigen-antibody complexes, especially at the contact interface, and markedly improves the binding affinity of generated antibodies.