Partner prediction based on a restricted conformational space.

because of no common residue between the small predicted interface and the docked one); hence, we cleaned the original Mintseris dataset of these three complexes and marked the affected subsets with the * symbol. Performance of protein prediction is evaluated through AUC values computed on the Mintseris dataset and its different subsets. Sensitivity () and specificity () are also given at a threshold cutoff of 0.5 for predictions based on experimental interfaces, and at a threshold cutoff of 0.25 for predicted interfaces. Calculations based on JET predicted interfaces use weights , (see Methods), with the exception of the analysis run for Antibody-Antigen and Antigen-Bound Antibody where , . The analysis is realized by assuming knowledge of either the experimental interfaces or the predicted interfaces. In both cases, we report the results obtained on the restricted (by evolutionary information) conformational space. On three complexes (1ML0, 1GCQ, 1DFJ), JET provided too small interaction sites (leading to a