urokinase COMBINE model with solvation terms and corrected Ki values

ligands: X-ray conformations of urokinase complexes

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

final urokinase COMBINE model

testing the model with docked ligands

no-dbl-Ki	no-dbl_ki-A20-A29	final1	Katz	Strzebecher	Wendt	set1	set2	set3	set4	set5
30	28	26	12	6	9	17	17	18	13	13
A04 A12 A13 A14 A15 A16 A17 A18 A19 A21 A20 A22 A23 A24 A25 A26 A28 A29 A30 A31 A32 A33 A34 A35 A36 A37 A38 A39 A40 A41	A04 A12 A13 A14 A15 A16 A17 A18 A19 A21 A22 A23 A24 A25 A26 A28 A30 A31 A32 A33 A34 A35 A36 A37 A38 A39 A40 A41	A04 A12 A13 A14 A15 A16 A17 A18 A19 A21 A22 A23 A24 A26 A30 A31 A32 A33 A34 A35 A36 A37 A38 A39 A40 A41	A04 A12 A13 A14 A15 A16 A17 A18 A19 A21 A23 A24	A25 A26 A28 A39 A40 A41	A30 A31 A32 A33 A34 A35 A36 A37 A38	A12 A13 A15 A16 A18 A19 A22 A23 A26 A30 A32 A33 A35 A36 A38 A39 A41	A04 A13 A14 A16 A17 A19 A21 A23 A24 A30 A31 A33 A34 A36 A37 A39 A40	A04 A12 A14 A15 A17 A18 A21 A22 A24 A26 A31 A32 A34 A35 A37 A38 A40 A41	A04 A13 A15 A17 A19 A22 A24 A30 A32 A34 A36 A38 A40	A12 A14 A16 A18 A21 A23 A26 A31 A33 A35 A37 A39 A41

file	#	LV	XAccum	R	SDEC	r2	SDEP	q2	selection	LV	XAccum	R	SDEC	r2	SDEP	q2
no-dbl_ki	30	1 2 3 4 5 6 7 8 9 10	44.5509 62.5665 73.1424 79.2187 83.0818 86.0039 88.4328 90.9105 92.5376 93.6349	0.6461 0.8995 1.0990 0.9792 1.5743 2.0828 1.9133 1.0747 1.0068 1.1036	1.4039 1.1246 0.9264 0.7632 0.6897 0.5901 0.5300 0.4972 0.4379 0.4110	0.2998 0.5508 0.6951 0.7931 0.8310 0.8763 0.9002 0.9122 0.9319 0.9400	1.6044 1.5527 1.5970 1.5976 1.5521 1.4673 1.4666 1.4454 1.5122 1.6160	0.0855 0.1436 0.0940 0.0933 0.1443 0.2352 0.2360 0.2578 0.1877 0.0723	D8F8 no-dbl_ki.ps	1 2 3 4 5 6 7 8 9 10	33.9779 53.8904 71.2340 80.9194 85.1923 88.2825 90.3499 92.1007 93.5181 94.7112	0.8397 1.2544 0.8852 0.7887 6.1648 1.4612 1.9452 1.0862 1.4179 1.1035	1.2877 1.0862 0.7906 0.6707 0.5952 0.5863 0.5621 0.5158 0.4496 0.4089	0.4110 0.5809 0.7780 0.8402 0.8742 0.8779 0.8878 0.9055 0.9282 0.9406	1.5745 1.4683 1.2686 1.1368 1.0382 0.9756 0.9493 1.1016 1.2994 1.4816	0.1193 0.2341 0.4283 0.5409 0.6171 0.6619 0.6798 0.5689 0.4002 0.2202
no-dbl_ki-A20-A29	28							0.0172
final1 (test5-A25-28.dat)	26	1 2 3 4 5 6 7 8 9 10	48.2587 68.1613 77.3882 81.8637 84.9804 87.7089 89.9040 92.2830 93.4791 94.6019	0.6263 0.8132 8.9280 1.4642 1.4189 1.4426 1.2385 1.2359 1.5429 1.1159	1.2628 0.9951 0.8629 0.7404 0.6413 0.5611 0.5109 0.4375 0.4014 0.3364	0.2805 0.5532 0.6640 0.7527 0.8144 0.8579 0.8822 0.9136 0.9273 0.9489	1.4295 1.3213 1.2529 1.1931 1.3708 1.5552 1.8249 2.1079 2.2369 2.5542	0.0779 0.2123 0.2917 0.3578 0.1521 -0.0913 -0.5027 -1.0047 -1.2576 -1.9436	D4F4 final1_d4f4_ pred5.png final1_d4f4_ partial_weight.png	1 2 3 4 5 6 7 8 9 10	53.9784 75.5756 86.4838 90.2410 91.8186 93.3859 94.5115 95.3955 96.2554 96.8500	0.6124 0.6832 1.4816 0.9329 5.4205 1.9384 25.2159 1.2684 0.9606 1.3176	1.2422 0.9707 0.8430 0.7099 0.6200 0.5415 0.4607 0.4049 0.3541 0.3268	0.3037 0.5749 0.6793 0.7726 0.8266 0.8677 0.9042 0.9260 0.9434 0.9518	1.3930 1.2094 1.1086 0.9567 0.9183 0.9549 1.0052 1.0801 1.1080 1.1382	0.1245 0.3400 0.4454 0.5870 0.6195 0.5886 0.5441 0.4737 0.4461 0.4155
final1-buw		3						0.2484	with BUW no better results than without
Katz	12							0.0830
Strzebecher	6	1 2 3 4	49.1131 73.7768 90.2656 95.4428	0.7401 34.8902 0.2648 0.5645	0.2856 0.1466 0.0749 0.0013	0.9538 0.9878 0.9968 1.0000	0.5579 0.5459 0.5720 0.5419	0.8238 0.8313 0.8148 0.8338	stuerzi2_pred1.png
Wendt	9							-
set1	17	3						0.1169
set2	17	4				0.7910	1.2028	0.2239
set3	18	4	80.9451		0.5741	0.8703	1.0991	0.5249
set4	13							-
set5	13	1 2 3 4 5	50.8217 69.6755 77.4136 83.4992 88.3866	0.5609 0.8637 10.3950 17.8731 211.3251	1.1740 0.7278 0.5692 0.4058 0.2601	0.4022 0.7702 0.8595 0.9286 0.9707	1.5062 1.2734 1.2187 1.1978 1.2487	0.0161 0.2967 0.3558 0.3778 0.3237	prediction for set4 D4F4 set5_d4f4_pred.png no better prediction for set4	1 2 3 4 5 6	67.6303 77.7384 84.6323 89.7860 92.5998 94.4095	0.3589 0.8189 1.0108 3.9976 1.9021 1.0732	1.2235 0.5357 0.3868 0.2680 0.1773 0.1095	0.3507 0.8755 0.9351 0.9689 0.9864 0.9948	1.4715 0.9963 0.8274 0.8142 0.7274 0.6962	0.0609 0.5694 0.7031 0.7125 0.7705 0.7898

no-dbl_ki.ps

final1_d4f4_pred5.png

final1_d4f4_partial_weight.png

stuerzi2_pred1.png

set5:

prediction of set4
External PLS predictions for /home/henricsn/combine2go/data/urokinase/prep-anal/model/model5_xray_medium/golpe-ki-neu/set4.dat
1 A19.0
Exper: -9.105 Pred:( 1 ) -8.112 ( 2 ) -6.738 ( 3 ) -6.519 ( 4 ) -6.391 ( 5 ) -6.404

12 A22.0
Exper: -6.147 Pred:( 1 ) -8.045 ( 2 ) -7.644 ( 3 ) -7.898 ( 4 ) -7.976 ( 5 ) -8.166

13 A13.0
Exper: -7.228 Pred:( 1 ) -7.566 ( 2 ) -7.815 ( 3 ) -7.101 ( 4 ) -7.078 ( 5 ) -7.085

18 A24.0
Exper: -7.39 Pred:( 1 ) -8.305 ( 2 ) -8.19 ( 3 ) -8.234 ( 4 ) -7.947 ( 5 ) -7.773

22 A15.0
Exper: -9.077 Pred:( 1 ) -8.045 ( 2 ) -9.36 ( 3 ) -9.135 ( 4 ) -9.288 ( 5 ) -9.325

23 A04.0
Exper: -9.739 Pred:( 1 ) -8.107 ( 2 ) -9.505 ( 3 ) -9.311 ( 4 ) -9.288 ( 5 ) -9.227

25 A17.0
Exper: -10.2 Pred:( 1 ) -8.023 ( 2 ) -9.583 ( 3 ) -9.156 ( 4 ) -9.465 ( 5 ) -9.807

26 A32.0
Exper: -11.18 Pred:( 1 ) -8.698 ( 2 ) -8.783 ( 3 ) -9.389 ( 4 ) -9.304 ( 5 ) -9.567

28 A34.0
Exper: -10.09 Pred:( 1 ) -8.821 ( 2 ) -9.198 ( 3 ) -9.959 ( 4 ) -9.866 ( 5 ) -10.25

30 A36.0
Exper: -9.979 Pred:( 1 ) -8.597 ( 2 ) -9.331 ( 3 ) -9.995 ( 4 ) -9.574 ( 5 ) -9.62

34 A30.0
Exper: -10.17 Pred:( 1 ) -8.557 ( 2 ) -7.345 ( 3 ) -7.484 ( 4 ) -8.326 ( 5 ) -8.429

36 A38.0
Exper: -8.021 Pred:( 1 ) -8.544 ( 2 ) -8.196 ( 3 ) -8.433 ( 4 ) -8.215 ( 5 ) -8.456

37 A40.0
Exper: -10.3 Pred:( 1 ) -11.21 ( 2 ) -11.92 ( 3 ) -11.71 ( 4 ) -11.21 ( 5 ) -11.29

Y_1 Components SDEP (external)
0 1.4867
1 1.4510
2 1.4394
3 1.3687
4 1.2347
5 1.2078

set5_d4f4_pred.png

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