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Abstract: Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The antibody binding affinity is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins, which closely interact with antigen residues (epitopes). In this talk, I will present new generative models to automatically design the CDRs of antibodies with desired binding affinity. Specifically, our model seeks to co-design the sequence and 3D structure of CDRs as graphs. It unravels a sequence auto regressively while iteratively refining its predicted global 3D structure. Our model is evaluated on binder design tasks and shows superior performance compared to existing baselines.

Speaker: Wengong Jin - http://people.csail.mit.edu/wengong/ 

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