On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
Fig 5
PPV for residue-residue contact prediction from natural data and Null model II.
The positive predictive values for residue contact prediction are shown for datasets DS2 (Panels A and C) and DS3 (Panels B and D), using the natural data (red, blue) and randomized data from Null model II (green). The upper panels (A,B) show joint contact prediction for all proteins, the lower panels (C,D) the averages over the individual PPV curves for all single families. All panels show also hypothetical PPV curves (purple), which might be reached by a method removing phylogenetic biases; they articficially combine DCA scores obtained from natural MSA on contacts, and from Null model I on non-contacts.