Table 2.
Consensus docking methods.
| Source | T a | Posing b | F c | Consensus Strategy | Analysis | Ref. |
|---|---|---|---|---|---|---|
|
DUD-E/
PDB |
102/3 | 4 | 4 | Standard Deviation Consensus (SDC), Variable SDC (vSDC) |
Rank/Score curves Hit recovery count |
Chaput, 2016 [121] |
| DUD-E | 21 | 8 | 8 | Gradient Boosting | EF, ROCAUC | Ericksen, 2017 [124] |
|
PDBBind
DUD |
228/1 | Vina, AutoDock | 2 | Compound rejection if pose RMSD > 2.0 Å | Success rate | Houston, 2013 [114] |
| PDB | 3 | GAsDock | 2 | Multi-Objective Scoring Function Optimisation | EF | Kang, 2019 [108] |
| mTOR d Inhibitors | 1 | Glide | 26 | Linear Combination | BEI Correlation | Li, 2018 [119] |
| PDB | 220 | FlexX | 9 | Several e | Compression and Accuracy | Oda, 2006 [120] |
| DUD-E | 102 | Dock 3.6 | 15 | Genetic Algorithm used to combine SF components | EF, BEDROC | Perez-Castillo, 2019 [116] |
| PDBBind | 1300 | 7 | 7 | RMSD-based pose consensus, multivariate linear regression | Success rate | Plewczynski, 2011 [115] |
| DUD | 35 | 10 | 10 | Compound rejection based on RMSD consensus level | EF | Poli, 2016 [112] |
| PDBBind | 3535 | 11 | 11 | Selection of representative pose with minimum RMSD | Success rate | Ren, 2018 [111] |
| PDB | 100 | AutoDock | 11 | Supervised Learning (Random Forests), Rank-by-rank |
Average RMSD, Success rate |
Teramoto, 2007 [125] |
|
PDB
DUD |
130/3 | 10 | 10 | Compound rejection based on RMSD consensus level | EF, ROCAUC | Tuccinardi (2014) [113] |
| PDBBind CSAR | 421 | Glide | 7 | Support Vector Rank Regression | Top pose /Top Rank | Wang, 2013 [126] |
| PDB | 4 | GEMDOCK GOLD |
2 | Rank-by-rank, Rank-by-score |
Rank/Score curve, GH Score, CS index | Yang, 2005 [127] |
a Total number of targets used in the assay; b Posing software used. If more than two software were used, than only the number is indicated; c Number of scoring functions used; d In this study, the dataset was composed of 25 mammalian target of rapamycin (mTOR) kinase inhibitors retrieved from the literature and six mTOR crystal structures retrieved from PDB; e The purpose of this study was to evaluate several different consensus strategies (e.g., rank-by-vote, rank-by-number, etc).