Figure 3. Effect of lysine constraints on the accuracy of topology prediction.

Effect of constraints on the topology prediction accuracy of CCTOP on the experimental benchmark set. (A) Prediction accuracy versus percent of extracellular lysines used as constraints in the prediction. 0, 4, 8, 12, 16% of the used extracellular lysines were replaced by intracellular lysines (blue, green, orange, red and black line, respectively) (B). Predictions were sorted according to their reliability values, then the accuracies were calculated on proteins with the largest 1, 2, 3 … 333 reliability values, represented as coverage from 0 to 100% on the x-axis of the plot. The colors of the curves are coded according to the ratio of randomly selected extracellular lysine (blue, green, orange, red and black for 100, 75, 50, 25 and 0%, respectively). Averages are plotted with continuous lines, standard deviations are shaded.