urokinase COMBINE model with solvation terms

receptor: urokinase model5-cut.pdb

ligands: X-ray conformations of urokinase complexes

minimization: medium constraints
UHBD input: desolv1_35.inp, desolv2_35.inp


set1
 set2
 set4
 set5
 set6
 set7
A19
A21
A20
A25
A26
A28
A12
A22
A13
A18
A16
A35
A36
A37
A41
A29
A30
A31
A38
 A24
A14
A23
A15
A04
A17
A32
A33
A34
A40
 A19
A21
A20
A25
A26
A12
A22
A13
A18
A16
A14
A23
A15
A04
A17
A33
A34
A35
A36
A37
A29
A30
A31
A38
A40
 A28
A24
A32
A41
A39
 A19
A20
A28
A12
A16
A24
A23
A15
A04
A32
A33
A36
A37
A41
A29
A40
 A21
A25
A26
A22
A13
A18
A14
A17
A34
A35
A30
A31
A38
A39
Different sets of ligands used for validation of the model. The ligands A25 and A28 were determined as outliers. For benzamidine (A20) very different Ki values were reported. A29 has the lowest Ki, much lower than others. For this reason A20 and A29 are also treated as outliers.
no-dbl: all ligands with given Ki, but alernative conformations of the ligands weren't used.
buw: set with used block unweight scale

file #
 PC
 XAccum
 R
 r2
 q2
 SDEP
 selection
 PC
 XAccum
 R
 r2
 q2
no-dbl 30 6
 86.0039 2.0828 0.8529 0.3069
D6/F6 6
 91.4922 0.8239 0.8533 0.6498
set4
 25
 2
4
 55.2375
75.1522
 53.0630
0.9881
 0.6507
0.8180
 0.3797
0.2333
D2/F2
D4/F4
 5
4
 84.7154
80.9533
 1.0322
0.8901
 0.8649
0.8487
 0.4947
0.6336
set4,-A25
 24
 2
5
6
 57.5141
81.8327
85.4208
 43.0171
1.2466
1.2931
 0.6845
0.8722
0.8930
 0.4419
0.4482
0.4542		 1.2131
1.2062
1.1997
 no realy
improve-
ment




set1
 18



-






set1-buw
 18



-






set1-A28-A42
 16
 2
 52.5433
 1.0331
 0.7187
 0.2529
F2
 1
4
 40.0581
84.3052
 1.1454
0.8463
 0.6576
0.8623
 0.4567
0.3467
set2
 11
 4
 94.2158
 0.8302
 0.9333
 0.5697
D4/F4
 4
 96.2327
 0.6612
 0.9378
 0.7510
set6
 16



-






set7
 14



0.09






no_outliers
(no_dbl, -A29, -A28,
-A39, -A41)
 26
 2

0.54
 0.1788






no_dbl-A29
 29



0.09






no_dbl-A29-buw 29
 8


0.1774






no_dbl-amidino-A29
 27
 7


0.1481






no_dbl-amidino
 28
 7


0.36







no-dbl: With BUW or FFD with D-selection no better results.

set1-A28-A42: gives good prediction (PC3, SDEP 0.7135 kcal/mol) for training set 'set2' (except for A23).
set2: for test set 'set1' PC3, SDEP 1.6617.

testing the training set no-dbl with docked ligands

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