19.09.2005 /scratch/mcm/henricsn/nochmal/
proteins: ~/combine2go/data/urokinase/pdb/prepared/
ligands: ~/combine2go/data/urokinase/pdb/ligand/rename/
programs:
xleap.sh (23.08.05)
local_sxleap.sh (19.09.05)
prep_interaction.sh (16.09.05)
calc_interaction.sh (22.09.05)
dielec=4

22.09.05
In script calc_interaction.sh were wrong variable settings with overwriting existing *.outa files.
New calculation!

COMBINE model with several alternative conformations
COMBINE model with one alternative conformation of each complex
Docking solutions
COMBINE model with receptor model5 and best ChemScore ranked docking solutions of ligands with known X-ray structures
Prediction of binding energy of docking solutions

Amber8

New minimization of all uPA X-ray complex structures (receptor and ligand conformations were taken from X-ray structures):

The RMSD is calculated between the X-ray and minimized ligand structure.
1c5w.1 RMSD 0.907
1c5w.2 RMSD 0.552
1c5x.1 RMSD 0.856
1c5x.2 RMSD 0.794
1c5y.01 RMSD 1.155
1c5y.02 RMSD 1.169
1c5z.0 RMSD 0.843
1ejn.0 RMSD 1.003
1f5k.0 RMSD 1.173
1f5l.0 RMSD 1.177
1f92.0 RMSD 2.100
1gi7.1 RMSD 0.794
1gi7.2 RMSD 1.409
1gi8.0 RMSD 2.356
1gi9.0 RMSD 2.284
1gj7.1 RMSD 2.443
1gj7.2 RMSD 1.617
1gj8.0 RMSD 2.264
1gj9.11 RMSD 2.476 no activity for uPA
1gj9.12 RMSD 2.608 no activity for uPA
1gj9.21 RMSD 2.702 no activity for uPA
1gj9.22 RMSD 2.243 no activity for uPA
1gja.0 RMSD 1.221
1gjb.1 RMSD 2.091
1gjb.2 RMSD 2.187
1gjc.1 RMSD 2.447
1gjc.2 RMSD 2.446
1gjd.0 RMSD 2.888
1o3p.1 RMSD 2.193
1o3p.2 RMSD 2.130
1o5a.0 RMSD 2.670
1o5b.1 RMSD 0.715
1o5b.2 RMSD 0.634
1o5c.1 RMSD 2.704
1o5c.2 RMSD 2.679
1owd.0 RMSD 2.284
1owe.0 RMSD 1.255
1owh.0 RMSD 1.706
1owi.0 RMSD 2.245
1owj.0 RMSD 1.961
1owk.0 RMSD 2.233
1sc8.0 RMSD 1.587
1sqa.0 RMSD 2.564
1sqo.0 RMSD 1.674
1sqt.0 RMSD 2.454
1u6q.0 RMSD 1.649
1vj9.0 RMSD 1.518
1vja.0 RMSD 1.541
TOTAL BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB EELNB HBOND CONSTRAINT TOTAL
1c5w.1 52.24 456.6 2166.82 893.96 858.59 -2145.24 -1461.97 0 0 821.003
1c5w.2 51.85 457.26 2166.18 894.62 858.76 -2146.16 -1464.65 0 0 817.833
1c5x.1 52.19 459.19 2173.42 896.74 858.97 -2137.33 -1470.77 0 0 832.406
1c5x.2 52.94 458.52 2172.69 896.2 858.78 -2137.91 -1471.08 0 0 830.141
1c5y.01 52.74 466.68 2172.11 900.33 862.86 -2135.58 -1465.91 0 0 853.222
1c5y.02 54.01 466.03 2170.84 899.81 862.73 -2133.84 -1465.9 0 0 853.676
1c5z.0 49.63 450.73 2167.19 895.68 865.18 -2124.94 -1467 0 0 836.484
1ejn.0 46.98 431.9 2186.38 864.51 820.26 -2192.57 -1415.97 0 0 741.499
1f5k.0 53.46 433.2 2150.51 840.77 837.05 -2163.93 -1425.17 0 0 725.896
1f5l.0 48.56 420.6 2157.96 845.09 813.7 -2184.68 -1413.8 0 0 687.419
1f92.0 50.62 438.86 2224.88 876.15 834.61 -2188.22 -1426.41 0 0 810.486
1gi7.1 57.79 464.14 2168.95 905.29 863.66 -2142.76 -1466.27 0 0 850.788
1gi7.2 57.91 470.47 2171.49 904.82 870.22 -2141.75 -1463.92 0 0 869.238
1gi8.0 47.41 497.26 2175.34 922.66 872.76 -2126.28 -1473.31 0 0 915.837
1gi9.0 48.8 479.26 2174.05 907.46 862.89 -2137.64 -1477.56 0 0 857.259
1gj7.1 50.32 480.11 2196.1 912.75 859.21 -2163.57 -1485.16 0 0 849.768
1gj7.2 50.16 478.79 2194.32 912.89 859.19 -2165.97 -1485.94 0 0 843.447
1gj8.0 47.18 469.2 2170.49 908.67 865.51 -2158.43 -1476.41 0 0 826.207
1gj9.11 48.41 480.27 2205.78 916.77 862.06 -2177.44 -1487.77 0 0 848.07
1gj9.21 48.8 475.15 2203 916.57 865.41 -2178.81 -1488.11 0 0 842.015
1gja.0 47.64 440.64 2160.8 901.37 848.65 -2169.59 -1460.43 0 0 769.08
1gjb.1 54.82 486.22 2196.44 924.78 865.61 -2120.88 -1478.56 0 0 928.435
1gjb.2 55.28 485.22 2194.9 925.12 865.64 -2119.63 -1479.28 0 0 927.254
1gjc.1 52.19 480.27 2197.45 918.92 866.8 -2139.87 -1472.34 0 0 903.425
1gjc.2 52.08 479.31 2195.54 919.36 866.7 -2141.54 -1472.7 0 0 898.745
1gjd.0 44.79 449.08 2163.46 921.24 860.2 -2175.34 -1474.48 0 0 788.952
1o3p.1 50.54 481.09 2204.32 926.02 863.58 -2140.58 -1484.85 0 0 900.114
1o3p.2 50.08 483.87 2203.4 926.01 868.02 -2143.1 -1481.78 0 0 906.492
1o5a.0 51.38 489.95 2200.87 907.78 858.76 -2157.47 -1479.16 0 0 872.116
1o5b.1 52.24 462.53 2167.14 898.63 861.91 -2143.2 -1457.7 0 0 841.551
1o5b.2 52.24 459.34 2168.09 898.62 860.92 -2142.13 -1459.48 0 0 837.61
1o5c.1 49.09 484.95 2190.23 899.48 858.68 -2180.28 -1480.54 0 0 821.614
1o5c.2 49.51 484.28 2191.08 899.58 858.52 -2178.71 -1483.67 0 0 820.589
1owd.0 64.13 440.71 2133.38 845.05 832.54 -2129.52 -1393.25 0 0 793.052
1owe.0 77.63 466.39 2167.08 828.38 822.98 -2188.93 -1412.52 0 0 761.004
1owh.0 80.74 467.46 2164.76 828.31 831.54 -2194.31 -1420.89 0 0 757.613
1owi.0 63.9 447.09 2153.37 860.53 825.48 -2087.5 -1387.1 0 0 875.763
1owj.0 68.67 452.85 2167.93 869.27 837.94 -2036 -1355.81 0 0 1004.851
1owk.0 62.95 446.92 2150.59 849.43 828.27 -2102.33 -1376.76 0 0 859.078
1sc8.0 54.95 411.66 2176.65 866.82 830.71 -2166.09 -1436.38 0 0 738.319
1sqa.0 70.85 494.38 2176.08 852.03 827.86 -2182.39 -1425.28 0 0 813.537
1sqo.0 69.29 480.12 2173.67 839.7 826.36 -2177.44 -1424.84 0 0 786.852
1sqt.0 78.55 510.53 2215.34 827.69 821.22 -2214.3 -1407.84 0 0 831.178
1u6q.0 57.33 452.29 2140.18 842.09 837.84 -2148.29 -1404.75 0 0 776.694
1vj9.0 46.09 416.59 2180.64 880.35 839.04 -2183.23 -1436.17 0 0 743.309
1vja.0 53.19 420.66 2182.71 873.26 844.07 -2177.64 -1450.21 0 0 746.044

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golpe

Interaction energy calculation in anal with more than alternative conformation of each crystal structure complex.

xray-min.dat containts all the minimized structures above without 1gj9. Compare to uPA-trypsin_310105 were just some of these structures were selected:

Data file : /home/henricsn/combine2go/data/urokinase/prep-anal/xray-min_ohne_wasser/golpe2/xray-min.dat
Comment : Extraction from output.dat
Number of variables = 496
Number of experiments = 44

Number of X-variables = 490 , Y-variables = 1
Loading :
1 1c5w.1
2 1c5w.2
3 1c5x.1
4 1c5x.2
5 1c5y.01
6 1c5y.02
7 1c5z.0
8 1ejn.0
9 1f5k.0
10 1f5l.0
11 1f92.0
12 1gi7.1
13 1gi7.2
14 1gi8.0
15 1gi9.0
16 1gj7.1
17 1gj7.2
18 1gj8.0
23 1gja.0
24 1gjb.1
25 1gjb.2
26 1gjc.1
27 1gjc.2
28 1gjd.0
29 1o3p.1
30 1o3p.2
31 1o5a.0
32 1o5b.1
33 1o5b.2
34 1o5c.1
35 1o5c.2
36 1owd.0
37 1owe.0
38 1owh.0
39 1owi.0
40 1owj.0
41 1owk.0
42 1sc8.0
43 1sqa.0
44 1sqo.0
45 1sqt.0
46 1u6q.0
47 1vj9.0
48 1vja.0

Active X-variables (SS 1.0E-7) = 217
Active Y-variables (SS 1.0E-7) = 1
Active X-variables after PRETREATMENT = 217
Active Y-variables after PRETREATMENT = 1

Principal Component Analysis (PCA) 44 objects 217 X-var
components XVarExp XAccum
1 30.2709 30.2709
2 25.3486 55.6195
3 14.1525 69.7720
4 7.2886 77.0606
5 4.8905 81.9511
6 3.2934 85.2445
7 2.8315 88.0760
8 2.0340 90.1099
9 1.8251 91.9350
10 1.2496 93.1846

PCA Rank Validation - using 4 random groups
components PRESS Seps R
1 7.7136e+02 9.0130e+02 0.8558
2 5.6279e+02 6.1260e+02 0.9187
3 3.2746e+02 3.7984e+02 0.8621
4 3.2424e+02 2.5189e+02 1.2872
5 1.7973e+02 1.8599e+02 0.9663
6 1.6997e+02 1.4229e+02 1.1945
7 5.1643e+02 1.1303e+02 4.5689
8 8.6569e+01 8.8691e+01 0.9761
9 6.7645e+01 7.1370e+01 0.9478
10 5.5024e+01 5.6420e+01 0.9753

Partial Least Squares (PLS) 44 objects 217 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.2693 0.0000
1 24.1534 24.1534 5.1591 0.3228
2 14.1094 38.2628 4.3119 0.5270
3 18.2362 56.4990 3.5033 0.6877
4 14.2398 70.7388 3.2041 0.7388
5 2.9701 73.7089 2.8758 0.7896
6 5.1792 78.8881 2.6989 0.8147
7 3.0393 81.9274 2.5719 0.8317
8 0.9210 82.8484 2.1968 0.8772
9 4.0945 86.9429 2.0467 0.8934
10 2.2270 89.1699 1.8900 0.9091

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.4151 - -0.0471
1 5.8951 - 0.1158
2 6.3288 - -0.0191
3 5.7252 - 0.1660
4 5.4934 - 0.2322
5 4.9472 - 0.3773
6 5.0418 - 0.3533
7 5.0033 - 0.3631
8 5.1783 - 0.3178
9 5.3205 - 0.2798
10 5.5658 - 0.2118

Deleted unselected vars. (D-Optimal)
1 : 217 - 108 Comp.=5 , Thu Sep 22 17:52:04 2005
Active X-variables after VAR. SELECT. = 108

*** FFD Variable Selection Started ***
Max. dimensionality : 5
Validation Mode : LOO
Recalculate weights : yes
Comb./Var. ratio : 2.0
Use groups :
Uncertains : Retain
Fold-over design : no
perc. of dummies : 20
Deleted unselected vars. (F.Factorial)
1 : 108 - 91 Comp.=5 , Thu Sep 22 17:52:23 2005
Active X-variables after VAR. SELECT. = 91

Principal Component Analysis (PCA) 44 objects 91 X-var
components XVarExp XAccum
1 40.8200 40.8200
2 21.0299 61.8499
3 14.3975 76.2474
4 5.6878 81.9352
5 3.8912 85.8264
6 3.4176 89.2440
7 2.0081 91.2521
8 1.6787 92.9308
9 1.1062 94.0370
10 0.9945 95.0315

PCA Rank Validation - using 4 random groups
components PRESS Seps R
1 4.2372e+02 4.8086e+02 0.8812
2 2.5351e+02 2.7739e+02 0.9139
3 1.3040e+02 1.7420e+02 0.7486
4 9.2666e+01 1.0560e+02 0.8775
5 8.4137e+01 7.8142e+01 1.0767
6 5.0927e+01 5.9615e+01 0.8543
7 5.7004e+01 4.3959e+01 1.2968
8 3.3660e+01 3.4714e+01 0.9696
9 2.8437e+01 2.7217e+01 1.0448
10 2.2612e+01 2.2256e+01 1.0160

Partial Least Squares (PLS) 44 objects 91 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.2693 0.0000
1 40.5264 40.5264 5.1721 0.3194
2 2.6983 43.2247 3.3534 0.7139
3 18.3128 61.5374 3.1408 0.7490
4 6.7693 68.3067 2.8702 0.7904
5 12.2723 80.5790 2.7876 0.8023
6 5.7039 86.2829 2.6641 0.8194
7 1.5509 87.8338 2.3775 0.8562
8 3.1234 90.9572 2.2448 0.8718
9 1.2984 92.2556 2.0332 0.8948
10 1.2171 93.4727 1.8848 0.9096

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.4151 - -0.0471
1 5.7137 - 0.1694
2 6.0360 - 0.0730
3 4.4340 - 0.4998
4 4.0373 - 0.5853
5 4.1856 - 0.5543
6 4.2606 - 0.5381
7 4.2288 - 0.5450
8 4.2765 - 0.5347
9 4.3094 - 0.5275
10 4.4641 - 0.4930

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For the following COMBINE model just one alternative conformations were used from each X-ray complex structure:

Data file : /home/henricsn/combine2go/data/urokinase/prep-anal/xray-min_ohne_wasser/golpe2/xray-min_no_double.dat

Comment : Extraction from xray-min.dat

Number of variables = 496
Number of experiments = 34

Number of X-variables = 490 , Y-variables = 1
Loading :

2 1c5w.2
3 1c5x.1
6 1c5y.02
7 1c5z.0
8 1ejn.0
9 1f5k.0
10 1f5l.0
11 1f92.0
12 1gi7.1
14 1gi8.0
15 1gi9.0
17 1gj7.2
18 1gj8.0
23 1gja.0
24 1gjb.1
27 1gjc.2
28 1gjd.0
29 1o3p.1
31 1o5a.0
33 1o5b.2
34 1o5c.1
36 1owd.0
37 1owe.0
38 1owh.0
39 1owi.0
40 1owj.0
41 1owk.0
42 1sc8.0
43 1sqa.0
44 1sqo.0
45 1sqt.0
46 1u6q.0
47 1vj9.0
48 1vja.0

Active X-variables (SS 1.0E-7) = 217
Active Y-variables (SS 1.0E-7) = 1

Active X-variables after PRETREATMENT = 217
Active Y-variables after PRETREATMENT = 1


Principal Component Analysis (PCA) 34 objects 217 X-var

components XVarExp XAccum
1 30.9834 30.9834
2 23.2616 54.2451
3 15.4128 69.6579
4 7.4486 77.1065
5 5.4546 82.5611
6 3.5898 86.1509
7 2.1987 88.3496
8 2.1119 90.4615
9 1.4433 91.9048
10 1.3197 93.2245



PCA Rank Validation - using 4 random groups

components PRESS Seps R
1 7.0907e+02 7.5983e+02 0.9332
2 5.9713e+02 5.0748e+02 1.1767
3 2.6911e+02 3.2525e+02 0.8274
4 3.3467e+02 2.0831e+02 1.6067
5 1.9450e+02 1.5162e+02 1.2829
6 1.0498e+02 1.1128e+02 0.9434
7 2.8756e+02 8.5042e+01 3.3814
8 6.9652e+01 6.8749e+01 1.0131
9 5.9837e+01 5.4010e+01 1.1079
10 4.4825e+01 4.3912e+01 1.0208


Partial Least Squares (PLS) 34 objects 217 X-var 1 Y-var

Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.2685 0.0000
1 25.6053 25.6053 5.0220 0.3582
2 23.6482 49.2535 4.6633 0.4466
3 7.4723 56.7258 3.7179 0.6482
4 9.0066 65.7324 3.2853 0.7253
5 10.7452 76.4777 3.0329 0.7659
6 3.8952 80.3729 2.7277 0.8106
7 1.7236 82.0965 2.4737 0.8443
8 1.2010 83.2975 2.0768 0.8902
9 5.1169 88.4144 1.8981 0.9083
10 1.6316 90.0460 1.5641 0.9377


PLS Model Validation - LOO

Y1 components SDEP SDEV(sdep) q2
0 6.4584 - -0.0615
1 5.9466 - 0.1001
2 6.1919 - 0.0243
3 6.5007 - -0.0755
4 6.0154 - 0.0791
5 6.0283 - 0.0752
6 5.9752 - 0.0914
7 6.0475 - 0.0693
8 6.0506 - 0.0683
9 6.4038 - -0.0437
10 6.6368 - -0.1210


Deleted unselected vars. (D-Optimal)
1 : 217 - 108 Comp.=6 , Fri Sep 23 13:36:56 2005
Active X-variables after VAR. SELECT. = 108


*** FFD Variable Selection Started ***
Max. dimensionality : 6
Validation Mode : LOO
Recalculate weights : yes
Comb./Var. ratio : 2.0
Use groups :
Uncertains : Retain
Fold-over design : no
perc. of dummies : 20


Deleted unselected vars. (F.Factorial)
1 : 108 - 92 Comp.=6 , Fri Sep 23 13:37:12 2005
Active X-variables after VAR. SELECT. = 92



Principal Component Analysis (PCA) 34 objects 92 X-var

components XVarExp XAccum
1 45.6029 45.6029
2 16.3458 61.9488
3 14.5554 76.5041
4 6.7672 83.2713
5 3.2940 86.5653
6 3.1820 89.7473
7 1.5664 91.3136
8 1.2011 92.5147



PCA Rank Validation - using 4 random groups

components PRESS Seps R
1 9.7391e+02 3.6453e+02 2.6717
2 1.9881e+02 1.9189e+02 1.0360
3 9.3978e+01 1.2977e+02 0.7242
4 6.2015e+01 7.7387e+01 0.8014
5 5.4545e+01 5.3152e+01 1.0262
6 3.8741e+01 4.1129e+01 0.9419
7 4.8280e+01 3.0205e+01 1.5984
8 1.8569e+02 2.4591e+01 7.5510
9 8.3377e+01 2.0334e+01 4.1004
10 8.2894e+01 1.6674e+01 4.9716


Partial Least Squares (PLS) 34 objects 92 X-var 1 Y-var

Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.2685 0.0000
1 45.3530 45.3530 5.1137 0.3345
2 3.2764 48.6295 3.5134 0.6859
3 13.4874 62.1169 3.1968 0.7399
4 6.7802 68.8970 2.8258 0.7968
5 10.6580 79.5550 2.5775 0.8309
6 7.3009 86.8559 2.4586 0.8462
7 0.6776 87.5335 1.9607 0.9022
8 2.9668 90.5003 1.7691 0.9204


PLS Model Validation - LOO

Y1 components SDEP SDEV(sdep) q2
0 6.4584 - -0.0615
1 5.7396 - 0.1616
2 6.2284 - 0.0128
3 4.5522 - 0.4726
4 4.2824 - 0.5333
5 4.2650 - 0.5371
6 4.4019 - 0.5069
7 4.6348 - 0.4533
8 4.6126 - 0.4585
9 4.8223 - 0.4082
10 4.9494 - 0.3766

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Docking solutions

COMBINE model with receptor model5 and best ChemScore ranked docking solutions of ligands with known X-ray structures

~/combine2go/data/urokinase/pdb/gold/uPA-docking/temp19/ranked_PDB_uPA_300805_3D_m_best_sort.sdf
uPA receptor model: model5.pdb
Scoring function: ChemScore

1 A04.1
2 A12.2
3 A13.3
4 A14.4
5 A15.5
6 A16.6
7 A17.7
8 A18.8
9 A19.9
10 A20.10
11 A21.11
12 A22.12
13 A23.13
14 A24.14
15 A25.15
16 A26.16
17 A30.19
18 A31.20
19 A32.21
20 A33.22
21 A35.24
22 A36.25
23 A37.26
24 A38.27
25 A39.28
26 A28.17
27 A40.29
28 A29.18
29 A34.23
30 A41.30

Wrong binding mode:
16 A26.16
26 A28.17

Data file : /home/henricsn/combine2go/data/urokinase/prepared/model/model5_docked_xray/golpe/dock-min_no_outliers.dat
Comment : Extraction from output.dat
Number of variables = 516
Number of experiments = 28
Number of X-variables = 510 , Y-variables = 1
Loading :
1 A04.1
2 A12.2
3 A13.3
4 A14.4
5 A15.5
6 A16.6
7 A17.7
8 A18.8
9 A19.9
10 A20.10
11 A21.11
12 A22.12
13 A23.13
14 A24.14
15 A25.15
17 A30.19
18 A31.20
19 A32.21
20 A33.22
21 A35.24
22 A36.25
23 A37.26
24 A38.27
25 A39.28
27 A40.29
28 A29.18
29 A34.23
30 A41.30

Active X-variables (SS 1.0E-7) = 204
Active Y-variables (SS 1.0E-7) = 1

Principal Component Analysis (PCA) 28 objects 204 X-var
components XVarExp XAccum
1 27.4467 27.4467
2 20.7950 48.2417
3 13.5493 61.7910
4 8.0926 69.8837
5 6.8568 76.7405
6 6.5013 83.2417
7 3.0476 86.2893
8 2.4654 88.7547
9 1.3599 90.1146
10 1.3951 91.5097

PCA Rank Validation - using 4 random groups
components PRESS Seps R
1 1.9381e+03 4.8632e+02 3.9853
2 3.1383e+02 3.3911e+02 0.9255
3 2.0778e+02 2.3215e+02 0.8950
4 6.1810e+03 1.6420e+02 37.6429
5 2.6997e+02 1.2379e+02 2.1809
6 8.2570e+01 9.1266e+01 0.9047
7 6.0832e+01 6.2643e+01 0.9711
8 4.7060e+01 4.8713e+01 0.9661
9 4.4490e+01 3.7881e+01 1.1745
10 3.1221e+01 3.1484e+01 0.9916

Partial Least Squares (PLS) 28 objects 204 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.6682 0.0000
1 19.1095 19.1095 4.9080 0.4583
2 17.7843 36.8937 4.3426 0.5759
3 15.2269 52.1206 3.8282 0.6704
4 11.4674 63.5881 3.3532 0.7471
5 5.1283 68.7164 2.8785 0.8137
6 3.8244 72.5408 2.3526 0.8755
7 5.3987 77.9396 1.9389 0.9155
8 3.6347 81.5742 1.4912 0.9500
9 5.3193 86.8935 1.1736 0.9690
10 2.4796 89.3731 0.9286 0.9806

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.9152 - -0.0754
1 6.1665 - 0.1448
2 6.2823 - 0.1124
3 6.7204 - -0.0157
4 7.2748 - -0.1902
5 7.2923 - -0.1959
6 7.7985 - -0.3677
7 8.4000 - -0.5869
8 8.5417 - -0.6408
9 8.6514 - -0.6833
10 8.3987 - -0.5863

Deleted unselected vars. (D-Optimal)
1 : 204 - 102 Comp.=2 , Wed Sep 28 16:07:15 2005
Active X-variables after VAR. SELECT. = 102

*** FFD Variable Selection Started ***
Max. dimensionality : 2
Validation Mode : LOO
Recalculate weights : yes
Comb./Var. ratio : 2.0
Use groups :
Uncertains : Retain
Fold-over design : no
perc. of dummies : 20
Deleted unselected vars. (F.Factorial)
1 : 102 - 93 Comp.=2 , Wed Sep 28 16:07:29 2005
Active X-variables after VAR. SELECT. = 93

Principal Component Analysis (PCA) 28 objects 93 X-var
components XVarExp XAccum
1 34.1413 34.1413
2 20.9651 55.1064
3 11.1759 66.2823
4 8.3203 74.6027
5 5.0757 79.6783

PCA Rank Validation - using 4 random groups
components PRESS Seps R
1 8.1937e+02 3.1842e+02 2.5732
2 1.8278e+02 2.0155e+02 0.9069
3 1.2546e+02 1.3184e+02 0.9516
4 1.2470e+02 9.4874e+01 1.3144
5 7.1618e+01 6.8350e+01 1.0478
6 5.2959e+01 5.2209e+01 1.0144
7 9.7972e+01 3.9760e+01 2.4641
8 3.8300e+01 3.2461e+01 1.1799
9 3.1481e+01 2.6959e+01 1.1677
10 2.6912e+01 2.2369e+01 1.2031

Partial Least Squares (PLS) 28 objects 93 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.6682 0.0000
1 25.2702 25.2702 4.7291 0.4970
2 27.5458 52.8160 4.3211 0.5801
3 4.8363 57.6523 3.3600 0.7461
4 7.7152 65.3675 2.9707 0.8015
5 4.9975 70.3651 2.5153 0.8577

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.9152 - -0.0754
1 5.6700 - 0.2770
2 5.7340 - 0.2606
3 6.2303 - 0.1270
4 6.0784 - 0.1691
5 6.2676 - 0.1165
6 6.8192 - -0.0458
7 6.7878 - -0.0362
8 6.8246 - -0.0475
9 6.6122 - 0.0167
10 6.0124 - 0.1870

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Prediction of binding energy of docking solutions with COMBINE model consisting of minimized X-ray structures with several alternative conformations

The minimized model5-docked ligand compelex structures were cut to the same length as the receptor chains of the complexes of the X-ray COMBINE model.

best q2 at PC5

External PCA predictions for /home/henricsn/combine2go/data/urokinase/prepared/model/model5_docked_xray/golpe-cut/output.dat
% SS explained for each object and model dimensionality
1 A04.1 2.84 9.73 25.64 36.44 42.59 47.69 50.98 51.01 51.21 55.32
2 A12.2 35.98 36.00 36.52 36.94 38.23 41.60 70.93 71.09 71.66 72.49
3 A13.3 27.23 36.12 36.46 36.55 38.16 51.40 57.66 65.75 66.28 70.34
4 A14.4 13.65 21.82 36.22 36.28 41.59 46.18 46.58 51.38 51.65 52.22
5 A15.5 1.93 9.94 24.40 24.49 46.01 58.50 60.91 64.24 64.25 64.91
6 A16.6 0.93 6.40 26.30 31.64 37.65 45.92 59.23 60.07 60.36 63.46
7 A17.7 10.37 19.67 41.29 41.92 59.34 68.33 71.36 74.52 75.36 76.28
8 A18.8 10.06 17.95 28.27 28.70 48.52 59.20 60.07 64.39 65.25 71.09
9 A19.9 72.59 74.56 78.62 78.98 87.04 87.36 88.96 91.06 91.07 92.07
10 A20.10 72.67 73.81 78.74 78.86 81.17 83.98 85.29 92.20 92.74 94.78
11 A21.11 71.26 73.81 75.48 75.65 80.17 81.49 81.60 82.69 82.70 82.71
12 A22.12 27.44 36.50 36.63 36.70 37.58 52.84 54.24 67.35 68.27 70.93
13 A23.13 30.36 32.56 51.38 61.35 64.22 70.96 72.16 73.24 73.27 73.27
14 A24.14 1.41 1.63 2.81 4.02 4.36 6.59 6.84 9.18 26.40 28.20
15 A25.15 8.76 43.06 56.00 56.02 65.10 65.69 67.63 67.73 71.43 72.58
16 A26.16 4.97 11.28 18.63 21.30 23.54 33.86 33.98 36.51 55.96 64.53
17 A30.19 52.83 67.54 72.31 72.38 75.38 76.07 77.22 79.91 80.43 80.51
18 A31.20 22.21 51.64 51.71 60.01 61.29 62.81 62.85 63.33 63.35 63.35
19 A32.21 42.20 53.92 57.76 57.81 58.19 58.22 59.90 64.60 64.64 64.95
20 A33.22 53.69 62.08 66.88 67.02 67.58 67.62 67.81 78.36 79.50 79.61
21 A35.24 49.40 54.69 56.82 56.89 62.31 62.35 62.35 62.87 62.94 63.14
22 A36.25 52.38 58.60 60.66 60.76 66.53 66.56 66.57 66.92 67.06 67.20
23 A37.26 33.39 44.24 47.50 48.58 52.18 55.33 55.49 61.79 62.02 62.07
24 A38.27 0.07 2.96 5.11 7.13 20.87 26.51 30.47 40.04 41.77 42.74
25 A39.28 0.00 44.33 56.30 60.19 60.19 62.11 62.11 62.53 62.69 62.69
26 A40.29 34.73 68.36 74.99 75.02 76.44 79.95 80.00 80.66 80.76 81.29
27 A28.17 0.00 9.31 11.01 11.28 11.44 16.66 16.71 20.23 34.81 34.84
28 A29.18 16.97 18.38 19.20 30.96 44.04 44.61 45.69 46.03 49.68 54.07
29 A34.23 21.70 26.80 34.89 34.98 35.23 35.29 36.77 38.65 38.72 38.78
30 A41.30 0.50 24.09 30.09 31.41 33.59 33.99 34.35 39.16 39.97 39.98
components SSExp SSAccum
1 21.8835 21.8835
2 14.1419 36.0254
3 6.8826 42.9080
4 2.1866 45.0946
5 3.9826 49.0772
6 4.1054 53.1826
7 1.4267 54.6094
8 2.6754 57.2848
9 4.3558 61.6406
10 1.7768 63.4174

External PLS predictions for /home/henricsn/combine2go/data/urokinase/prepared/model/model5_docked_xray/golpe-cut/output.dat
1 A04.1
Exper: -40.75 Pred:( 1 ) -35.68 ( 2 ) -34.25 ( 3 ) -33.41 ( 4 ) -32.3 ( 5 ) -31.65
2 A12.2
Exper: -28.81 Pred:( 1 ) -33.69 ( 2 ) -25.71 ( 3 ) -24.53 ( 4 ) -22.72 ( 5 ) -22.38
3 A13.3
Exper: -29.79 Pred:( 1 ) -34.1 ( 2 ) -28.39 ( 3 ) -28.1 ( 4 ) -26.87 ( 5 ) -26.82
4 A14.4
Exper: -36.21 Pred:( 1 ) -37.48 ( 2 ) -35.46 ( 3 ) -34.94 ( 4 ) -34.66 ( 5 ) -34.02
5 A15.5
Exper: -37.98 Pred:( 1 ) -36.82 ( 2 ) -33.67 ( 3 ) -32.78 ( 4 ) -31.99 ( 5 ) -31.18
6 A16.6
Exper: -39.7 Pred:( 1 ) -36.47 ( 2 ) -31.11 ( 3 ) -29.94 ( 4 ) -28.36 ( 5 ) -27.49
7 A17.7
Exper: -42.68 Pred:( 1 ) -37.64 ( 2 ) -34.61 ( 3 ) -33.69 ( 4 ) -32.79 ( 5 ) -31.81
8 A18.8
Exper: -44.99 Pred:( 1 ) -37.66 ( 2 ) -38.17 ( 3 ) -38.02 ( 4 ) -38.67 ( 5 ) -38.44
9 A19.9
Exper: -38.1 Pred:( 1 ) -32.07 ( 2 ) -33.39 ( 3 ) -33.77 ( 4 ) -34.08 ( 5 ) -34.55
10 A20.10
Exper: -30.24 Pred:( 1 ) -31.85 ( 2 ) -27.02 ( 3 ) -26.69 ( 4 ) -26.35 ( 5 ) -26.81
11 A21.11
Exper: -23.96 Pred:( 1 ) -32.5 ( 2 ) -30.17 ( 3 ) -30.18 ( 4 ) -29.9 ( 5 ) -30.07
12 A22.12
Exper: -25.72 Pred:( 1 ) -34.1 ( 2 ) -28.95 ( 3 ) -28.89 ( 4 ) -28.18 ( 5 ) -28.24
13 A23.13
Exper: -29.79 Pred:( 1 ) -38.97 ( 2 ) -31.95 ( 3 ) -32.41 ( 4 ) -32.95 ( 5 ) -32.2
14 A24.14
Exper: -30.92 Pred:( 1 ) -35.87 ( 2 ) -33.1 ( 3 ) -32.75 ( 4 ) -32.21 ( 5 ) -31.6
15 A25.15
Exper: -32.06 Pred:( 1 ) -38.44 ( 2 ) -37.98 ( 3 ) -36.24 ( 4 ) -36.03 ( 5 ) -34.83
16 A26.16
Exper: -30.1 Pred:( 1 ) -34.55 ( 2 ) -40.27 ( 3 ) -39.46 ( 4 ) -40.67 ( 5 ) -41.07
17 A30.19
Exper: -42.53 Pred:( 1 ) -33.14 ( 2 ) -36.21 ( 3 ) -36.9 ( 4 ) -36 ( 5 ) -36.06
18 A31.20
Exper: -35.37 Pred:( 1 ) -33.92 ( 2 ) -37.37 ( 3 ) -38.4 ( 4 ) -36.27 ( 5 ) -36.12
19 A32.21
Exper: -39.01 Pred:( 1 ) -33.38 ( 2 ) -34.65 ( 3 ) -35.24 ( 4 ) -34.64 ( 5 ) -34.8
20 A33.22
Exper: -35.37 Pred:( 1 ) -32.83 ( 2 ) -31.34 ( 3 ) -31.32 ( 4 ) -29.84 ( 5 ) -29.77
21 A35.24
Exper: -39.84 Pred:( 1 ) -32.57 ( 2 ) -30.73 ( 3 ) -31.02 ( 4 ) -30.8 ( 5 ) -31.11
22 A36.25
Exper: -41.75 Pred:( 1 ) -32.62 ( 2 ) -30.99 ( 3 ) -31.34 ( 4 ) -31.16 ( 5 ) -31.48
23 A37.26
Exper: -43.52 Pred:( 1 ) -33.3 ( 2 ) -37.3 ( 3 ) -37.81 ( 4 ) -36.03 ( 5 ) -35.89
24 A38.27
Exper: -33.56 Pred:( 1 ) -36.13 ( 2 ) -32.92 ( 3 ) -32.26 ( 4 ) -31.31 ( 5 ) -30.67
25 A39.28
Exper: -43.92 Pred:( 1 ) -36.03 ( 2 ) -32.45 ( 3 ) -34.8 ( 4 ) -33.3 ( 5 ) -32.97
26 A40.29
Exper: -43.09 Pred:( 1 ) -41.17 ( 2 ) -42.84 ( 3 ) -45.02 ( 4 ) -43.36 ( 5 ) -42.21
27 A28.17
Exper: -35.33 Pred:( 1 ) -36.63 ( 2 ) -39.77 ( 3 ) -40.46 ( 4 ) -37.87 ( 5 ) -37.38
28 A29.18
Exper: -52.53 Pred:( 1 ) -39.12 ( 2 ) -42.2 ( 3 ) -41.05 ( 4 ) -37.99 ( 5 ) -37.26
29 A34.23
Exper: -42.2 Pred:( 1 ) -33.63 ( 2 ) -35.19 ( 3 ) -35.51 ( 4 ) -34.64 ( 5 ) -34.88
30 A41.30
Exper: -28.52 Pred:( 1 ) -36.32 ( 2 ) -29.81 ( 3 ) -30.97 ( 4 ) -30.59 ( 5 ) -30.16

Y_1 Components SDEP (external)
0 6.5631
1 6.5045
2 6.0925
3 6.0871
4 6.7670
5 6.9521

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23.09.2005
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