Results of COMBINE models


Comparing to former COMBINE models (run1-delwat2, uro1, uPA-trypsin_310105) some bugs in the scripts and programs were removed. Now, COMBINE models could be built for all the available uPA complex structures (except 1gj9, where no activity value could be found). In addition, the charges in the used SD file were corrected.

The best results could be achieved by using strong constraints for the minimization of the training set. This gave loweser RMSD for the ligands comparing to X-ray structures then with low constraints..
After variable selection (D-optimal preselection PC 10, F.Factorial selection PC 10) the best r2 and q2 (PC 7) was 0.85 and 0.59 (SDEP=4.0), respecitvely.



 X-ray Training set
strong constraints		 X-ray Test set
low constraints
 Docked Test set
docked structures
complexes
 46
30
after variable selection: D 10, FFD 10

PC
 7
 7 (9)
 2
r2
 0.8518

q2
 0.5919

SDEP
 4.0049
 4.0960 (3.9261)
 5.6762


04.10.05
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