The second CAPE paper demonstrates that direct preference optimization (DPO) can be used to fine-tune ProteinMPNN to generate protein designs predicted to be less visible to cytotoxic T lymphocytes, potentially reducing their autoimmunity risk
doi.org/10.1093/protei…
In this paper you can read all about the first steps towards CAPE - a suite of tools for the integration of immune-visibility targets into the computational protein design process
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