# Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction

arXiv: https://arxiv.org/abs/2608.01092 · HTML: https://mlsanity.com/paper/2608.01092/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 27 references that are in the map.
- First posted on arXiv 2 Aug 2026.

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Learning from Protein Structure with Geometric Vector Perceptrons](https://mlsanity.com/paper/2009.01411/) (2020)
- [Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking](https://mlsanity.com/paper/2111.07786/) (2021)
- [Deciphering antibody affinity maturation with language models and weakly supervised learning](https://mlsanity.com/paper/2112.07782/) (2021)
- [Neural message passing for joint paratope-epitope prediction](https://mlsanity.com/paper/2106.00757/) (2021)
- [AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction](https://mlsanity.com/paper/2407.18184/) (2024)

## Abstract (arXiv)

Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between antibody CDRs and the antigen surface. Existing methods usually leverage PLM embeddings and inject structure through additional graph, surface, or point-cloud encoders, where the positional mechanism inside attention remains largely tied to one-dimensional sequence order. For proteins, the analogue of a token offset is not only sequence separation, but also the three-dimensional displacement between residues after folding. This raises a question, can folded residue geometry serve as the positional mechanism of attention itself? We propose Local-Frame 3D Rotary Position Encoding (LF3DRoPE), which expresses inter-residue displacements in backbone-defined local frames and injects them directly into rotary attention. This design preserves continuous directional geometry while ensuring invariance to global SE(3) transformations. On the AsEP benchmark, LF3DRoPE achieves state-of-the-art MCC on both ratio and epitope-group splits. Ablations and rigid transformation tests show that local three-dimensional geometry provides information beyond sequence-order attention while preserving invariance to arbitrary global coordinate systems. Mutation ranking results further indicate that LF3DRoPE captures antigen-specific structural compatibility.