基于HelixFold3的蛋白结合物设计平台，实现高效自动化设计。
HelixDesign-Binder: A Scalable Production-Grade Platform for Binder Design Built on HelixFold3
- 以HelixFold3为基础，整合从骨架生成到序列设计的全流程
- 在6个靶点上验证，产出结合力媲美甚至超过已知设计的结合物
- 支持科研与工业应用，提供交互式网页界面，可大规模部署
蛋白质结合物设计在药物研发、诊断和合成生物学中至关重要，但实际应用受限于流程碎片化、计算成本高和工具集成复杂。我们提出HelixDesign-Binder，一个基于HelixFold3构建的生产级高通量平台，自动化完成从骨架生成、序列设计、结构评估到多维评分的完整流程。该平台通过统一各环节，实现高效探索具有优良结构、能量及理化性质的结合物候选。依托百度云高性能基础设施，支持大规模设计，并引入ipTM、预测结合自由能和界面疏水性等先进评分指标。在6个蛋白靶点上的基准测试表明，HelixDesign-Binder可稳定生成多样且高质量的结合物，部分设计在预测结合亲和力上达到或超越已有验证设计。平台可通过PaddleHelix平台的交互式网页界面访问，支持抗体与蛋白结合物研发的学术研究与工业应用。
原文摘要 · Abstract (English)
Protein binder design is central to therapeutics, diagnostics, and synthetic biology, yet practical deployment remains challenging due to fragmented workflows, high computational costs, and complex tool integration. We present HelixDesign-Binder, a production-grade, high-throughput platform built on HelixFold3 that automates the full binder design pipeline, from backbone generation and sequence design to structural evaluation and multi-dimensional scoring. By unifying these stages into a scalable and user-friendly system, HelixDesign-Binder enables efficient exploration of binder candidates with favorable structural, energetic, and physicochemical properties. The platform leverages Baidu Cloud's high-performance infrastructure to support large-scale design and incorporates advanced scoring metrics, including ipTM, predicted binding free energy, and interface hydrophobicity. Benchmarking across six protein targets demonstrates that HelixDesign-Binder reliably produces diverse and high-quality binders, some of which match or exceed validated designs in predicted binding affinity. HelixDesign-Binder is accessible via an interactive web interface in PaddleHelix platform, supporting both academic research and industrial applications in antibody and protein binder development.
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