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

TL;DR

HelixDesign-Antibody is a scalable, high-throughput platform built on HelixFold3 that streamlines antibody design by enabling large-scale sequence generation and interaction evaluation, significantly accelerating therapeutic development.

Contribution

The paper introduces a production-grade platform integrating HelixFold3 for high-throughput antibody design, addressing computational challenges and enabling large-scale exploration of antibody sequences.

Findings

Validated on multiple antigens with diverse antibody candidates.

Demonstrated a scaling law linking sequence space exploration to binder quality.

Achieved high-throughput screening with integrated HPC support.

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.