GOLD Validation: Results on an Additional 34 Complexes
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.
To view the GOLD prediction click on the PDB code in the table. 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 file 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 P
DB Group for allowing distribution of these data.
Results by ligand composition
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.
Second set of validation tests: Ligand characterisation
| 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
|
Second set of validation tests: Number of ligand rotatable bonds
| 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
|
| 
