Table 1.
The categorization and performance of theoretical methods of prediction of hydration structure.
| Method | Concept | Type a | #System/#Water b | Match Tolerance (Å) | SR (%) |
|---|---|---|---|---|---|
| 3D-RISM c [85,86,87] | Knowledge | IF | 18/113 d | 2.5 | 91 |
| IF | 13/113 e | 1.5 | 65 | ||
| SF | 8/101 e | 1.5 | 60 | ||
| AcquaAlta c [88] | Geometry | IF | 20/77 | 1.4 | 76 |
| Auto-SOL c [89] | Geometry | SF | 5/1337 | 1.5 | 64 |
| AQUARIUS f [90] | Knowledge | SF | 7/1376 | 1.4 | 59 |
| Fold-X c [91] | Energy | SF | 74/2687 | 1.0 | 76 |
| Forli et al., 2012 c [92] | Geometry g | IF | 27/51 | 2.0 | 96 |
| HADDOCK c [93] | Geometry g | IF | 27/50 | 2.0 | 90 |
| Huggins and Tidor, 2011 [94] | Geometry | IF | 5/19 | 2.0 | 68 |
| HydraMap c [95] | Dynamic | IF | 13/113 e | 1.5 | 72 |
| SF | 8/101 e | 1.5 | 69 | ||
| HyPred f [96] | Dynamic | SF | 3/233 | 1.0 | 12 |
| MobyWat c [13,40] | Dynamic | SF | 20/1500 | 1.5 | 80 |
| IF | 31/344 | 1.5 | 90 | ||
| Particle concept h [97] | Geometry | IF | 200/232 | 1.5 | 35 |
| Splash’Em c [98] | Knowledge | IF | 91/230 | 1.0 | 62 |
| SZMAP h [99] | Knowledge | IF | 18/113 d | 2.5 | 96 |
| WaterDock c [100] | Energy | SF | 7/92 | 2.0 | 88 |
| WaterFLAP h [87,101,102] | Knowledge | IF | 18/113 d | 2.5 | 98 |
| WaterMap h [37,87] | Dynamic | SF | 1/11 | 1.5 | 82 |
| IF | 18/113 d | 2.5 | 96 | ||
| WarPP c [103] | Geometry | IF | 1500/20,000 | 1.0 | 80 |
| WATGEN f [104] | Geometry | IF | 126/1264 | 2.0 | 88 |
| WATsite c [95,105] | Dynamic | IF | 13/113 e | 1.5 | 75 |
| SF | 8/101 e | 1.5 | 77 |
a Water molecules in the target–ligand interface (IF), and on unbound target surface (SF) are considered, respectively. b The count of systems/the count of experimental water oxygen positions used in the cited study for method validation. c Freeware or free trial for academic use. d These data are taken from the comparative paper [87]. e These data are taken from the paper [95]. f Website no longer available. g With docking search. h Commercially available.