Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction

• URL: http://arxiv.org/abs/2608.01092v1
• Date: Sun, 02 Aug 2026 08:48:07 GMT
• Title: Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction
• Abstract summary: Local-Frame 3D Rotary Position.<n>EPEP aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between CDRs and the antigen surface.<n>We propose Local-Frame 3D Rotary Position.<n>EPEP, which expresses inter-residue displacements in backbone-defined local frames and injects them directly into rotary attention.
• Score: 8.509019866126222
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: 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 $\mathrm{SE}(3)$ transformations. On the AsEP benchmark, LF3DRoPE achieves state-of-the-art $\mathrm{MCC}$ 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.

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