A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design

Abstract

Therapeutic antibodies are an essential and rapidly flourishing drug modality. The binding specificity between antibodies and antigens is decided by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a \textbf{h}ierarchical \textbf{t}raining \textbf{p}aradigm (HTP) for the antibody sequence-structure co-design. HTP consists of four levels of training stages, each corresponding to a specific protein modality within a particular protein domain. Through carefully crafted tasks in different stages, HTP seamlessly and effectively integrates geometric graph neural networks (GNNs) with large-scale protein language models to excavate evolutionary information from not only geometric structures but also vast antibody and non-antibody sequence databases, which determines ligand binding pose and strength. Empirical experiments show HTP sets the new state-of-the-art performance in the co-design problem as well as the fix-backbone design. Our research offers a hopeful path to unleash the potential of deep generative architectures and seeks to illuminate the way forward for the antibody sequence and structure co-design challenge.