Robust deep learning–based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A. +14 more·2022·Science

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  30. Generalizable and scalable protein stability prediction with rewired protein generative models
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