# RoBep: a region-oriented deep learning model for B-cell epitope prediction

## TL;DR

RoBep is a new deep learning model that improves B-cell epitope prediction by considering spatial clustering of residues, enhancing accuracy and biological relevance.

## Contribution

RoBep introduces a region constraint mechanism to model spatial clustering of epitope residues, improving prediction accuracy and biological plausibility.

## Key findings

- RoBep outperforms existing methods with improvements of up to 45% in key performance metrics.
- The model ensures predicted epitope residues are spatially compact, enhancing biological plausibility.
- RoBep provides both residue-level predictions and antibody–antigen binding regions.

## Abstract

Accurate in silico identification of B-cell epitope residues is crucial for antibody design and structure-guided vaccine development. Although recent protein language models and structure-aware methods can capture spatial information of tertiary structure when generating residue embeddings, most existing epitope predictors use these embeddings to perform classification for individual residues one by one, without enforcing spatial continuity for reported epitope residues. Such methods often result in biologically implausible predictions because B-cell epitope residues always cluster together on the antigen surface.

We present RoBep, a region-oriented B-cell epitope predictor that explicitly models the spatial clustering of epitope residues. RoBep introduces a novel region constraint mechanism and combines the advanced protein language model ESM-Cambrian with an equivariant graph neural network. Our method outperforms existing structure-based methods on the benchmark dataset, demonstrating improvements of 26%, 45%, 13%, and 43% in F1, Matthews correlation coefficient, area under the precision–recall curve, and AUROC0.1, respectively. In addition to residue-level predictions, RoBep can also provide antibody–antigen binding regions. Importantly, the predicted epitope residues are ensured to be spatially compact, enhancing biological plausibility and practical relevance for immunotherapeutic design.

A user-friendly website for using RoBep is provided at https://huggingface.co/spaces/NielTT/RoBep. All datasets, source code used in this work, and implementation instructions of the website are publicly available at https://github.com/YitaoXU/RoBep.