Table 1:
Docking programs available for RNA. Docking programs without dedicated binding site detection module are shown with a dash.
| Docking program | Target | Conformational search algorithm |
Binding site prediction |
|---|---|---|---|
| AutoDock Vina (66) | protein | Monte Carlo & quasi-Newton | - |
| GOLD (59) | protein | genetic algorithm | - |
| Glide (61) | protein | Monte Carlo | SiteMap (121) |
| AutoDock (98) | protein/RNA | genetic algorithm | AutoLigand (96) |
| ICM (97) | protein/RNA | Monte Carlo | PocketFinder (87) |
| DOCK 6 (65) | protein/RNA | incremental construction | sphgen module (95; 122) |
| FITTED (62) | protein/RNA | genetic algorithm | - |
| RiboDock (60) | RNA | genetic algorithm | two-sphere filter |
| rDock (67) | protein/RNA | genetic algorithm Monte Carlo simplex minimization | two-sphere filter |
| MORDOR (64) | RNA | molecular dynamics | grid-based systematic search |
| RLDOCK (70; 71) | RNA | multi-conformer docking | grid-based systematic search |