Table 1.
Comparison of shape-only and shape plus electrostatic docking correlations for the HyHel-5/lysozyme complex
| L | 1D shape-only |
1D shape+electro |
3D shape-only |
3D shape+electro |
5D shape-only |
5D shape+electro |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rank (RMS) | Time/m | Rank (RMS) | Time/m | Rank (RMS) | Time/m | Rank (RMS) | Time/m | Rank (RMS) | Time/m | Rank (RMS) | Time/m | |
| 16 | 646 (6.8) | 28.7 | 428 (8.0) | 52.0 | 864 (7.1) | 15.1 | 254 (8.2) | 18.1 | – | 37.5 | 669 (6.0) | 40.3 |
| 20 | 336 (1.2) | 52.7 | 20 (1.3) | 102.7 | 410 (1.2) | 23.5 | 17 (1.3) | 29.2 | 336 (7.9) | 39.3 | 29 (1.3) | 46.5 |
| 24 | 417 (1.2) | 92.4 | 52 (1.2) | 184.2 | 501 (1.2) | 33.2 | 53 (1.2) | 51.2 | 833 (1.2) | 53.0 | 82 (1.2) | 56.2 |
| 26 | 49 (1.2) | 123.3 | 15 (1.2) | 243.1 | 48 (1.2) | 43.5 | 15 (1.6) | 69.0 | 45 (1.2) | 58.7 | 13 (1.6) | 63.1 |
| 28 | 54 (1.5) | 158.1 | 8 (1.2) | 315.6 | 22 (5.2) | 54.2 | 11 (1.3) | 92.2 | 19 (5.5) | 64.5 | 13 (1.2) | 71.7 |
| 30 | 113 (2.2) | 203.5 | 43 (1.3) | 403.0 | 47 (1.6) | 69.8 | 20 (1.6) | 122.5 | 61 (1.6) | 74.3 | 19 (1.6) | 108.0 |
In the table L is the polynomial order of the expansion, Rank is the rank of the first orientation found in which the ligand is within 10 Å RMS (shown in parentheses) of the crystal structure after clustering with the default Hex clustering threshold. A hyphen indicates no near-native orientation found within the top 2000 solutions. Time is the total computation time in minutes on a single processor 1.8 GHz Pentium Xeon PC. The 3D and 5D FFT calculations used Kiss FFT. For those calculations, the time spent within the FFT library is essentially constant at 13.1 and 34.3 min, respectively. All timings exclude the calculation of the translation matrix elements.