Final summary
table
description
Excel tables
uPA uPA-all_040706.xls
(31.07.06, 17:10)
thrombin thrombin-all_040706.xls (28.07.06, 17:57)
trypsin trypsin-all_040706.xls
(28.07.06, 17:57)
sheets for comparing the three models compare-all_040706.xls
(28.07.06, 17:54)
some figures: Figures_Tables.pdf
(31.07.06, 17:27)
urokinase
training x-ray structures
active-nodbl-A25-A28-A29.dat
active-nodbl-A25-A28-A29.dat.VarType
active-nodbl-A25-A28-A29.dat.VarNames
docking
uPA-model7
gold_protein.mol2 (receptor model, mol2 from gold)
all_docked_all_040706_3D.sdf
(docking solutions)
uPA_all1_040706.dat.gz
uPA_all1_040706.dat.VarType.gz
uPA_all1_040706.dat.VarNames.gz
Data
file :
/home/henricsn/combine2go/data/urokinase/model7_060706/anal/active-nodbl-A25-A28-A29.dat
Comment :
Extraction from active-nodbl.dat
Number of
variables = 500
Number of
experiments = 26
Number of
X-variables = 492 , Y-variables = 1
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) 26 objects
217 X-var
PCA Rank
Validation - using 4 random groups
Partial Least
Squares (PLS) 26
objects 217 X-var 1
Y-var
PLS Model
Validation - LTO
PLS Model
Validation - LOO
components
XVarExp XAccum
PRESS Seps
R
XVarExp
XAccum SDEC
r2 SDEP
SDEV(sdep) q2
SDEP SDEV(sdep) q2
components
XVarExp XAccum
PRESS Seps
R
0.0000
0.0000 1.5105 0.0000 1.5721
-
-0.0833 1.5709 -
-0.0816
1 38.3794
38.3794 5.3841e+02 6.6993e+02
0.8037 28.7265
28.7265 1.0398 0.5262
1.2476 -
0.3178 1.2468
-
0.3187
2 18.0712
56.4506 4.0426e+02 3.9550e+02
1.0222 25.2363
53.9628 0.8577 0.6775
1.0895 -
0.4797 1.0856
-
0.4834
3 16.6936
73.1441 2.4480e+02 2.6732e+02
0.9158 5.2930
59.2558 0.6450 0.8177
0.9854 -
0.5744 0.9784
-
0.5805
4 5.1301
78.2743 1.1796e+03 1.5736e+02
7.4960 16.6667
75.9225 0.6181 0.8325
0.9317 -
0.6195 0.9145
-
0.6334
5 4.3520
82.6263 1.3871e+02 1.2127e+02
1.1438 3.2530
79.1755 0.5606 0.8623
1.1450 -
0.4254 1.1173
-
0.4528
6 3.5968
86.2231 2.4440e+02 9.2167e+01
2.6517 1.6721
80.8476 0.4517 0.9106
1.5455 -
-0.0469 1.5604
-
-0.0672
7 2.5769
88.8000 1.9908e+02 6.9289e+01
2.8731 4.4009
85.2485 0.4068 0.9275
1.7623 -
-0.3613 1.7976
-
-0.4163
8 2.2029
91.0029 6.3099e+02 5.3255e+01
11.8484 1.5489
86.7974 0.3149 0.9565
1.8404 -
-0.4846 1.8558
-
-0.5095
9 1.5990
92.6019 4.5525e+01 4.0320e+01
1.1291 1.6213
88.4187 0.2602 0.9703
1.8998 -
-0.5819 1.9178
-
-0.6121
10 1.5356
94.1375 4.2394e+01 3.1140e+01
1.3614 1.4308
89.8495 0.2262 0.9776
1.9079 -
-0.5954 1.9110
-
-0.6007
Deleted
unselected vars. (D-Optimal)
1
: 217 - 108 Comp.=4 , Wed Jul 19 10:25:30 2006
Active
X-variables after VAR. SELECT. = 108
*** FFD
Variable Selection Started ***
Max.
dimensionality : 4
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 - 97 Comp.=4 , Wed Jul 19 10:26:15
2006
Active
X-variables after VAR. SELECT. = 97
Principal
Component Analysis (PCA) 26 objects
97 X-var
PCA Rank
Validation - using 4 random groups
Partial Least
Squares (PLS) 26
objects 97 X-var 1 Y-var
PLS Model
Validation - LTO
PLS Model
Validation - LOO
components
XVarExp XAccum PRESS
Seps
R
XVarExp XAccum SDEC
r2
SDEP
SDEV(sdep) q2
SDEP
SDEV(sdep) q2
components
XVarExp XAccum PRESS
Seps
R
0.0000 0.0000
1.5105 0.0000 1.5721
-
-0.0833 1.5709
- -0.0816
1 41.0685
41.0685 3.4927e+02 5.1095e+02
0.6836 28.4718
28.4718 1.0176
0.5462 1.2188
- 0.3489
1.2170 -
0.3509
2 18.7558
59.8243 2.7262e+02 2.8848e+02
0.9450 29.6456
58.1174 0.8487
0.6843 1.0629
- 0.5048
1.0588 -
0.5086
3 17.7649
77.5892 1.2998e+02 1.8809e+02
0.6911 4.6665
62.7839 0.6244
0.8291 0.9227
- 0.6269
0.9112 -
0.6361
4 4.6575
82.2467 6.7473e+02 1.0015e+02
6.7370 14.3810
77.1649 0.6041
0.8400 0.8689
- 0.6691
0.8589 -
0.6767
5 3.3472
85.5939 1.2040e+03
7.5577e+01 15.9311 7.5697
84.7346
0.5693 0.8580 0.9079
-
0.6387 0.8981
- 0.6465
6 3.2218
88.8157 2.6200e+02 5.8288e+01
4.4949 1.1988
85.9334 0.4569
0.9085 1.1279
- 0.4424
1.1143 -
0.4558
7 2.1857
91.0013 4.7897e+01 4.2901e+01
1.1164 0.9897
86.9231 0.3612
0.9428 1.1798
- 0.3899
1.1897 -
0.3796
8 1.8078
92.8092 1.4290e+02 3.2634e+01
4.3789 1.2441
88.1672 0.3266
0.9533 1.1018
- 0.4679
1.0720 -
0.4963
9 1.8688
94.6779 2.1728e+01 2.4578e+01
0.8840 1.3406
89.5078 0.2878
0.9637 1.0816
- 0.4873
1.0232 -
0.5411
10 1.0099
95.6879 1.4885e+01 1.7085e+01
0.8713 3.1212
92.6290 0.2717
0.9676 1.1692
- 0.4008
1.1150 -
0.4551
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