# Towards More Accurate Full-Atom Antibody Co-Design

arXiv: https://arxiv.org/abs/2502.19391 · HTML: https://mlsanity.com/paper/2502.19391/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 9 of its 49 references that are in the map.
- First posted on arXiv 11 Feb 2025.

## Builds on (most cited first, 9 of 9)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [ProGen: Language Modeling for Protein Generation](https://mlsanity.com/paper/2004.03497/) (2020)
- [Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design](https://mlsanity.com/paper/2110.04624/) (2021)
- [Conditional Antibody Design as 3D Equivariant Graph Translation](https://mlsanity.com/paper/2208.06073/) (2022)
- [End-to-End Full-Atom Antibody Design](https://mlsanity.com/paper/2302.00203/) (2023)
- [AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies](https://mlsanity.com/paper/2308.05027/) (2023)
- [Inverse folding for antibody sequence design using deep learning](https://mlsanity.com/paper/2310.19513/) (2023)

## Built on by (most cited first, 1 of 1)

- [Multimodal QUD: Inquisitive Questions from Scientific Figures](https://mlsanity.com/paper/2604.23733/) (2026)

## Abstract (arXiv)

Antibody co-design represents a critical frontier in drug development, where accurate prediction of both 1D sequence and 3D structure of complementarity-determining regions (CDRs) is essential for targeting specific epitopes. Despite recent advances in equivariant graph neural networks for antibody design, current approaches often fall short in capturing the intricate interactions that govern antibody-antigen recognition and binding specificity. In this work, we present Igformer, a novel end-to-end framework that addresses these limitations through innovative modeling of antibody-antigen binding interfaces. Our approach refines the inter-graph representation by integrating personalized propagation with global attention mechanisms, enabling comprehensive capture of the intricate interplay between local chemical interactions and global conformational dependencies that characterize effective antibody-antigen binding. Through extensive validation on epitope-binding CDR design and structure prediction tasks, Igformer demonstrates significant improvements over existing methods, suggesting that explicit modeling of multi-scale residue interactions can substantially advance computational antibody design for therapeutic applications.