Fig. 3: Model captures sequence–structure relationship.

A, B Decoy ranking by model negative pseudo-log-likelihood (PLL) of the native sequence. A Model negative PLL vs. alpha-carbon RMSD (Å) to the native structure for Rosetta ab initio decoys. Points are colored by average side-chain RMSD to native (Å). In some cases, the model assigns low negative PLL to high RMS backbones; for example, for 1cc8 an alternative pattern of beta-strand pairing is shown (Inset). B Model negative PLL of low backbone RMS structures (CA RMSD < 5 Å) vs. average side-chain RMSD (Å). Box highlights low model negative PLL assigned to low side-chain RMSD decoys. C Spearman rank correlation between model negative PLL or Rosetta energy vs. structure alpha-carbon RMSD (Å) as a function of increasing RMSD cutoff. In the low RMS regime (<5 Å), the model and Rosetta are able to rank low RMS structures to a similar extent.