Fig. 3: TM-score difference to test conformation vs embedding difference for predictions with the highest TM-scores to the test and train conformations, respectively (n = 52).
From: Structure prediction of alternative protein conformations
a Comparison between TM-score and cosine similarity of the single sequence embeddings. b Comparison between TM-score and L2 difference of the pair embeddings. c Examples of predicted structures coloured by secondary structure (helix=cyan, loop=grey, sheet=magenta) with a big difference in predicted TM-score towards the test conformation, but both small and large cosine similarity. There appears to be no relationship between the variation in cosine similarity and the variation in structural similarity (conformational change).
