Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization

arXiv:2403.16576v1 Announce Type: cross
Abstract: Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nature. In this paper, we tackle antigen-specific antibody design as a protein sequence-structure co-design problem, considering both rationality and functionality. Leveraging a pre-trained conditional diffusion model that jointly models sequences and structures of complementarity-determining regions (CDR) in antibodies with equivariant neural networks, we propose direct energy-based preference optimization to guide the generation …

abstract antibody arxiv biology challenges cs.lg design energy nature optimization paper protein q-bio.bm therapeutics type via