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HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3

Jie Gao
Jing Hu
Shanzhuo Zhang
Kunrui Zhu
Sheng Qian
Yueyang Huang
Xiaonan Zhang
Xiaomin Fang
Main:10 Pages
7 Figures
Bibliography:2 Pages
Abstract

Antibody engineering is essential for developing therapeutics and advancing biomedical research. Traditional discovery methods often rely on time-consuming and resource-intensive experimental screening. To enhance and streamline this process, we introduce a production-grade, high-throughput platform built on HelixFold3, HelixDesign-Antibody, which utilizes the high-accuracy structure prediction model, HelixFold3. The platform facilitates the large-scale generation of antibody candidate sequences and evaluates their interaction with antigens. Integrated high-performance computing (HPC) support enables high-throughput screening, addressing challenges such as fragmented toolchains and high computational demands. Validation on multiple antigens showcases the platform's ability to generate diverse and high-quality antibodies, confirming a scaling law where exploring larger sequence spaces increases the likelihood of identifying optimal binders. This platform provides a seamless, accessible solution for large-scale antibody design and is available via the antibody design page of PaddleHelix platform.

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@article{gao2025_2507.02345,
  title={ HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3 },
  author={ Jie Gao and Jing Hu and Shanzhuo Zhang and Kunrui Zhu and Sheng Qian and Yueyang Huang and Xiaonan Zhang and Xiaomin Fang },
  journal={arXiv preprint arXiv:2507.02345},
  year={ 2025 }
}
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