Table I.
PAIRpred and PPiPP performance. We compare the performance of PAIRpred and PPiPP [9] using Area Under the ROC Curve (AUC) and the rank of the first positive prediction (RFPP). RFPP(p) indicates that p percent of the proteins achieve that level of performance. For example, on DBD 4.0 without post processing, the second PAIRpred prediction is part of the interface for 10% of the complexes. PAIRpred results are provided for two residue kernels: the sequence-based kernel, and for the kernel that uses all the features computed from sequence and structure.
| Dataset | Method | RFPP (p) | AUC | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 10% | 25% | 50% | 75% | 90% | Complex | Protein | |||
| DBD 3.0 (124 complexes) | PPiPP | 9 | 19 | 78 | 297 | 760 | 72.9 | 66.1 | |
| PAIRPred | |||||||||
| Kr = Kprofile + KprASA | No post-processing | 2 | 13 | 68 | 257 | 804 | 80.9 | 70.8 | |
| Kr = Kprofile + Kexp + KHSAAC + KCX | No post-processing | 1 | 5 | 22 | 89 | 282 | 87.3 | 73.4 | |
| With post-processing | 1 | 3 | 16 | 103 | 272 | 88.7 | 77.0 | ||
| DBD 4.0 (176 complexes) | Kr = Kprofile + Kexp + KHSAAC + KCX | No post-processing | 2 | 6 | 19 | 75 | 340 | 87.0 | 73.1 |
| With post-processing | 1 | 3 | 18 | 101 | 282 | 87.8 | 75.4 | ||