Jun Li

Jie Gao, Jun Li, Jing Hu et al.

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.

Xiaobo Jing, Jun Li, Xueping Zhao et al.

We present a set of linear, second order, unconditionally energy stable schemes for the Allen-Cahn equation with nonlocal constraints that preserves the total volume of each phase in a binary material system. The energy quadratization strategy is employed to derive the energy stable semi-discrete numerical algorithms in time. Solvability conditions are then established for the linear systems resulting from the semi-discrete, linear schemes. The fully discrete schemes are obtained afterwards by applying second order finite difference methods on cell-centered grids in space. The performance of the schemes are assessed against two benchmark numerical examples, in which dynamics obtained using the volumepreserving Allen-Cahn equations with nonlocal constraints is compared with those obtained using the classical Allen-Cahn as well as the Cahn-Hilliard model, respectively, demonstrating slower dynamics when volume constraints are imposed as well as their usefulness as alternatives to the Cahn-Hilliard equation in describing phase evolutionary dynamics for immiscible material systems while preserving the phase volumes. Some performance enhancing, practical implementation methods for the linear energy stable schemes are discussed in the end.