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La-Proteina
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Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. These changes involve how to map motif residues to sequence indices (different in indexed vs. unindexed) or how the exact features used as input to the model are built.
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