Correlation between structure and function not picked up by other methods. We applied three prediction methods to our dataset of structural effect: (A, D) the new method introduced here, (B, E) SNAP  predicting impact on function, and (C, F) I-Mutant3  predicting the impact on stability. In lack of a better alternative, we chose the default threshold for each method (horizontal dashed lines) to distinguish neutral from effect. The method introduced here that is specialized to separate structural effect from neutral performs best at this task (A: little overlap between boxes; note: data in cross-validation mode of our method). The distributions from SNAP (functional effect prediction) and I-Mutant3 (stability prediction) both do not capture the structure signal.
Schaefer and Rost BMC Genomics 2012 13(Suppl 4):S4 doi:10.1186/1471-2164-13-S4-S4