GAMA Miguel Angel @miangoar.bsky.social · Jul 9 1 / 2
6/9 So, the problem seems to be the seqs. What if we split by structures? Perhaps it gets better, but there are still issues like convergence (e.g. pockets of serinproteases or carbonic anhydrases) and fold switching (estimated to occur in ~4% of the PDB)
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7/9 So, what does OOD generalization mean? I don't know, but perhaps the answer lies in de novo proteins. In this paper, they applied fixed-backbone generation for various de novo designs and experimentally validated them, and their distribution is different from natural ones.