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All additional 34 complexes were selected at the Cambridge Crystallographic Data Centre. As before, the complexes were intended to be a diverse, unbiased and demanding test set for the program.
In the light of the first set of validation tests, the algorithm had been improved, particularly in order to deal with hydrophobic ligands.
In this second set of tests, GOLD achieved a 74% rate of successful prediction. In calculating this figure, the GOLD prediction is defined as the best of the 20 GA dockings according to the GOLD fitness score and not the docking that is closest to the experimental result.
Position of top ranked molecule
Each GOLD prediction was subjectively assigned to one of 4 categories: good, close, errors or wrong.
| Subjective Result | No | PDB Codes |
| Good | 12 | 1BMA 1CIL 1FRP 2GBP 1GLP 1LAH 1LPM 1MMQ 1MRG 1TRK 1TNL 1WAP |
| Close | 13 | 1ATL 1BBP 1BYB 1CBS 1COM 1FEN 1HFC 1IMB 1LCP 1NCO 1TNG 1TNI 1TPH |
| Errors | 6 | 2CMD 1CTR 2LGS 1LNA 1SNC 1UKZ |
| Wrong | 3 | 1CDG 1LMO 1TYL |
In order to reduce the size of the GOLD distribution directories, we have not included details of the individual predictions. However, these can be viewed in 3D on the Web pages of the Cambridge Crystallographic Data Centre. To view in 3D, you will need to download the Chime plug-in from the US MDL Web site or the uk site. The GOLD prediction is shown, together with the crystallographically observed position and conformation, both encoded in MDL MOL format. Coordinates of the test systems are available for downloading, so other groups are free to test their docking software on the same complexes. All file formats are SYBYL MOL2. Thanks are due to the Brookhaven PDB Group for allowing distribution of these data.
These tables show how the subjective result varies with the number of ligand atoms, the percentage of polar atoms in the ligand, and the number of ligand rotatable bonds and free corners.
| Subjective Result | Number of heavy atoms in ligand | % of heavy atoms which can form hydrogen bonds | ||||
| Max | Avg | Min | Max | Avg | Min | |
| Correct and close | 48 | 21.2 | 8 | 60.0 | 29.5 | 0.0 |
| Errors and wrong | 29 | 19.9 | 10 | 53.9 | 38.5 | 3.6 |
| Subjective Result | Max # of torsions | Avg # of torsions | Min # of torsions |
| Correct and close | 24 | 9.0 | 0 |
| Errors and wrong | 14 | 8.4 | 3 |