Table 4.
Performance of the state-of-the-art methods for RNA-binding site prediction.
| Methods | Data Set | Performance | Reference | Feature | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| ACC | SEN | SPE | AUC | MCC | Strength | F-Measure | Precision | ||||
| PiRaNhA | RB75 | - | - | - | 0.822 | 0.435 | - | - | - | [8] | Sequence-based |
| PPRInt | RB75 | - | - | - | 0.779 | 0.339 | - | - | - | [8] | |
| RB172 | 0.71 | - | 0.25 | 0.66 | - | - | [28] | ||||
| RB344 | 0.70 | 0.45 | 0.82 | 0.68 | 0.28 | - | 0.49 | 0.53 | [26] | ||
| BindN | RB75 | - | - | - | 0.733 | 0.297 | - | - | - | [8] | |
| RB172 | 0.75 | - | - | - | 0.23 | 0.64 | - | - | [28] | ||
| BindN+ | RB75 | - | - | - | 0.821 | 0.397 | - | - | - | [8] | |
| RB172 | 0.79 | - | - | - | 0.34 | 0.71 | - | - | [28] | ||
| RB344 | 0.72 | 0.32 | 0.89 | 0.68 | 0.26 | - | 0.41 | 0.56 | [26] | ||
| RNABindR | RB75 | - | - | - | 0.708 | 0.317 | - | - | - | [8] | |
| RNABindR v2.0 | RB172 | 0.66 | - | - | - | 0.27 | 0.69 | - | - | [28] | |
| PRBR | RB75 | - | - | - | N/A a | 0.294 | - | - | - | [8] | |
| NAPS | RB75 | - | - | - | 0.679 | 0.215 | - | - | - | [8] | |
| RB172 | 0.66 | - | - | - | 0.17 | 0.61 | - | - | [28] | ||
| RNAProB | RB172 | 0.82 | - | - | - | 0.22 | 0.60 | - | - | [28] | |
| KYG * | RB75 | - | - | - | N/A | 0.382 | - | - | - | [8] | Structure-based |
| DRNA * | RB75 | - | - | - | N/A | 0.382 | - | - | - | [8] | |
| RB344 | 0.75 | 0.21 | 0.94 | N/A | 0.22 | - | 0.31 | 0.54 | [26] | ||
| OPRA * | RB75 | - | - | - | N/A | 0.296 | - | - | - | [8] | |
| Ren’s method | RB344 | 0.68 | 0.48 | 0.76 | 0.68 | 0.26 | - | 0.48 | 0.48 | [26,83] | |
| Meta-predictor b | RB75 | - | - | - | 0.835 | 0.460 | - | - | - | [8,34] | |
a N/A—not available; MCC—Matthews Correlation Coefficient; AUC—area under curve; SEN—sensitivity; SPE—specificity; b Meta-predictor developed based on top three sequence-based methods according to authors benchmark (PiRaNhA, PPRInt and BindN+); * The meta-predictor is composed of those methods labeled with asterisk.