Table 1.
Benchmarked tool summary
| Tool (publication date) | Feature type | Computation model | Dataset (Train + Test) | Web server (YES / NO) | Code availability |
|---|---|---|---|---|---|
| Local-DPP [42] (23/06/2016) | Evolutionary | Classic | PDB1075 + PDB186 | NO | Not available |
| DNABP [43] (01/12/2016) | Sequence + Evolutionary | Classic | PDB14K (97%) + PDB14K (3%) | NO | Not available |
| iDNAProt-ES [37] (02/11/2017) | Sequence + Evolutionary + Structure | Classic | PDB1075 + PDB186 | YES | Not available |
| StackDPPred [44] (19/07/2018) | Evolutionary + Structure | Classic (stage) | PDB1075 + PDB186 | YES | Available but not runnable |
| PseAAC [45] (11/10/2018) | Sequence | Classic | PDB1075 + PDB186 | NO | Available |
| DeepDBP [46] (19/03/2020) | Sequence | Deep Learning | PDB1075 + PDB186 | NO | Partially available (no feature extraction) |
| PDBP-Fusion [24] (03/05/2021) | Sequence | Deep Learning | PDB14K + PDB2272 | NO | Not available |
| KK-DBP [47] (29/11/2021) | Evolutionary | Classic | PDB1075 + PDB186 | NO | Not available |
| LSTM-CNN_Fusion [23] (02/06/2022) | Sequence + Evolutionary | Deep Learning | PDB14K + PDB2272 | NO | Available |
| PB_DBP [35] (04/12/2023) | Sequence | Deep Learning | A custom dataset (80% + 20%) | NO | Not available |
| PreDBP-PLMs [34] (08/07/2024) | Sequence + Evolutionary | Deep Learning | PDB1075 + PDB186 PDB14K + PDB2272 | NO | Available |