# BConformeR: A Conformer Based on Mutual Sampling for Unified Prediction of Continuous and Discontinuous Antibody Binding Sites

arXiv: https://arxiv.org/abs/2508.12029 · HTML: https://mlsanity.com/paper/2508.12029/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 37 references that are in the map.
- First posted on arXiv 16 Aug 2025.

## Builds on (most cited first, 5 of 5)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Conformer: Convolution-augmented Transformer for Speech Recognition](https://mlsanity.com/paper/2005.08100/) (2020)
- [Conformer: Local Features Coupling Global Representations for Visual Recognition](https://mlsanity.com/paper/2105.03889/) (2021)

## Abstract (arXiv)

Accurate prediction of antibody-binding sites (epitopes) on antigens is crucial for vaccine design, immunodiagnostics, therapeutic antibody development, antibody engineering, research into autoimmune and allergic diseases, and advancing our understanding of immune responses. Despite in silico methods that have been proposed to predict both linear (continuous) and conformational (discontinuous) epitopes, they consistently underperform in predicting conformational epitopes. In this work, we propose Conformer-based models trained separately on AlphaFold-predicted structures and experimentally determined structures, leveraging convolutional neural networks (CNNs) to extract local features and Transformers to capture long-range dependencies within antigen sequences. Ablation studies demonstrate that CNN enhances the prediction of linear epitopes, and the Transformer module improves the prediction of conformational epitopes. Experimental results show that our model outperforms existing baselines in terms of MCC, ROC-AUC, PR-AUC, and F1 scores on both linear and conformational epitopes.