Figure 4.
Average RMSD [Å], Prob_score, difference in solvent accessible surface area [Å2] and secondary structure identity is plotted against SOM distance (binned from 0–4 in steps of 0.1). The SOM distance is defined as the average of the distances between locations in the three SOMs used in ProfNet_SS_SOM, for structurally aligned residue pairs (i.e. those used as positive examples in the neural network training). It can be seen that among the pairs that are close in the SOM space the average distance in the structural superposition is closer and that a higher fraction of these pairs have the same secondary structure. The Prob_score is also (inversely) correlated with SOM distance. In contrast no such clear trend can be found for the difference in surface accessibility.