(A) DeepContact outperforms CCMPred on the ASTRAL validation set using only CCMPred as features. Including other features further improves the precision-recall performance.
(B) Precision-recall performance of contact-prediction methods on the CAMEO dataset. DeepContact further outperforms metaPSICOV on the CAMEO dataset.
(C) Precision-recall performance of contact-prediction methods on the CASP228 dataset. On all three validation sets, using our novel probability cutoff enables enhancement of the precision/recall characteristics of DeepContact. Effectively, we exclude sequences or contacts with little confidence, and include contacts in which we have more confidence, leading to improved performance.
(D) The improved contact-prediction performance of DeepContact over CCMPred leads to improved contact-assisted folding across the CASP12 free-modeling target set. Targets where folding failed using CCMPred contacts are plotted at a TM-score of 0.