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arXiv · 2606.07567

SurfDesign: Effective Protein Design on Molecular Surfaces

Fang Wu·Shuting Jin·Xiangru Tang·Mark Gerstein·Xiangxiang Zeng·Yejin Choi·Jure Leskovec·Jinbo Xu
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Abstract

Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure. We introduce SurfDesign, a surface-conditioned protein design framework that models molecular surfaces as continuous geometric manifolds and integrates them with pretrained protein language models. SurfDesign employs surface-based equivariant message passing to capture surface normals, curvature, and directional geometry, together with a parameter-efficient fine-tuning strategy. Focusing on functional protein design, we show that SurfDesign consistently outperforms prior surface-conditioned and backbone-only methods on de novo binder and enzyme design benchmarks. We also report strong performance on inverse-folding benchmarks as a diagnostic of structural compatibility. Our results highlight manifold-aware surface representations as a principled foundation for functional protein and enzyme design. Code is available at https://github.com/smiles724/SurfDesign.

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Fang Wu, Shuting Jin, Xiangru Tang, Mark Gerstein, Xiangxiang Zeng, Yejin Choi, Jure Leskovec, Jinbo Xu. 2026-05-25. SurfDesign: Effective Protein Design on Molecular Surfaces. https://arxiv.org/abs/2606.07567

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