Benchmarks for residue-based PPI site prediction for proteins in the S58 dataset.

PredUs [28], [39] (http://bhapp.c2b2.columbia.edu/PredUs/) was unable to predict chain A of PDB ID 3myo and chain A of PDB ID 3ulc due to lack of “structural neighbors”. For the rest of the queries in PredUs predictions, the structural neighbor with PDB ID identical to the query protein was removed and the remaining structural neighbors were used for prediction. The PredUs predictions were compared with ANN_BAGGING prediction results as shown in the Table (detailed results are shown in Table S6). Only the prediction results for the protein surface residues (defined in Methods) were used for benchmarking. The benchmark measurements are defined in Equations (6)∼(11).