Table 3.
Timing results (in seconds) for (H) Hierarchical, (M) Middleman, (B) Brute force IMP for various sized molecules, where N is the number of atoms. “None” columns represent the molecule without any additional solvation layers. “Layer” includes additional atoms that form an 8Å water layer around the molecule. “Sphere” includes additional atoms from an 8Å water sphere around the molecule. Numbers in italics are estimated. Numbers written as a(b) indicate a number a × 10b.
| None | Layer | Sphere | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDB | N | D | H | M | B | N | D | H | M | B | N | D | H | M | B |
| 6LYZ | 1959 | 53 | 0.1 | 0.5 | 1.8 | 6785 | 70 | 0.4 | 2.2 | 22 | 16207 | 69 | 0.8 | 5.0 | 122 |
| 2R8S | 11556 | 161 | 1.0 | 12.7 | 65 | 35923 | 179 | 2.0 | 46 | 620 | 329765 | 178 | 12 | 419 | 5.2(3) |
| 3R8N | 93263 | 246 | 5.4 | 206 | 4.2(3) | 214840 | 263 | 9.5 | 533 | 2.2(4) | 1029628 | 262 | 40 | 2532 | 5.1(5) |
| 1FFK | 94876 | 240 | 5.7 | 201 | 4.3(3) | 256100 | 258 | 11 | 606 | 3.1(4) | 880941 | 256 | 37 | 2143 | 3.7(5) |
| 1AON | 118923 | 230 | 6.0 | 235 | 6.7(3) | 255198 | 247 | 11 | 565 | 3.1(4) | 845460 | 247 | 33 | 1875 | 3.4(5) |