bovine
trypsin model Data
file :
/home/henricsn/combine2go/data/trypsin/mod17_151205/golpe-bos/trypsin-model.dat Comment :
Extraction from set6.dat Number of
variables = 460 Number of
experiments = 11 Number of
X-variables = 452 , Y-variables = 1 Loading :
1
A13.0
2
A12.0
3
A18.0
4
A15.0
5
A01.0
6
A16.0
10
A09.0
12
A14.0
15
A50.0
18
A54.0
21
A57.0
Active
X-variables (SS 1.0E-7) = 178 Active
Y-variables (SS 1.0E-7) = 1 Active
X-variables after PRETREATMENT = 178 Active
Y-variables after PRETREATMENT = 1 Principal
Component Analysis (PCA) 11 objects
178 X-var
components XVarExp XAccum
1
40.4302 40.4302
2
30.1327 70.5629
3
12.5007 83.0636
4
5.3298 88.3935
5
3.2215 91.6150 PCA Rank
Validation - using 4 random groups
components
PRESS
Seps R
1
1.1972e+02 1.0948e+02
1.0935
2
3.4713e+01 5.8565e+01
0.5927
3
2.5567e+01 2.5668e+01
0.9961
4
5.2213e+01 1.2893e+01
4.0497
5
1.0377e+01 7.5566e+00
1.3732 Partial Least
Squares (PLS) 11
objects 178 X-var 1
Y-var Y1
components XVarExp
XAccum
SDEC r2
0
0.0000 0.0000
0.9557 0.0000
1
21.7946 21.7946
0.6042 0.6003
2
23.6972 45.4918
0.4157 0.8108
3
34.1669 79.6587
0.3193 0.8884
4
7.7870 87.4457
0.1961 0.9579
5
2.1612 89.6069
0.1028 0.9884 PLS Model
Validation - LOO Y1
components
SDEP
SDEV(sdep) q2
0
1.0512
- -0.2100
1
0.9365
- 0.0397
2
0.7556
- 0.3749
3
0.6945
- 0.4719
4
0.5691
- 0.6453
5
0.4999
- 0.7264 Deleted
unselected vars. (D-Optimal) 1
: 178 - 89 Comp.=3 , Tue Dec 20 15:46:33
2005 Active
X-variables after VAR. SELECT. = 89 *** FFD
Variable Selection Started *** Max.
dimensionality : 3 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
: 89 - 85 Comp.=3 , Tue Dec 20
15:46:47 2005 Active
X-variables after VAR. SELECT. = 85 Principal
Component Analysis (PCA) 11 objects
85 X-var
components XVarExp XAccum
1
39.2675 39.2675
2
30.6999 69.9674
3
12.1012 82.0686
4
8.8232 90.8918
5
2.1353 93.0271 PCA Rank
Validation - using 4 random groups
components
PRESS
Seps R
1
5.1968e+01 6.5337e+01
0.7954
2
3.5827e+01 3.5633e+01
1.0054
3
1.5925e+01 1.5628e+01
1.0189
4
5.2606e+00 8.1466e+00
0.6457
5
3.3621e+00 3.5390e+00
0.9500 Partial Least
Squares (PLS) 11
objects 85 X-var 1 Y-var Y1
components XVarExp
XAccum
SDEC r2
0
0.0000 0.0000
0.9557 0.0000
1
24.3708 24.3708
0.5000 0.7263
2
27.0035 51.3742
0.3478 0.8676
3
25.7237 77.0979
0.2123 0.9506
4
12.7091 89.8071
0.1812 0.9640
5
1.6435 91.4505
0.0963 0.9898 PLS Model
Validation - LOO Y1
components
SDEP
SDEV(sdep) q2
0
1.0512
- -0.2100
1
0.7711
- 0.3490
2
0.5793
- 0.6326
3
0.4598
- 0.7685
4
0.3986
- 0.8260
5
0.4613
- 0.7670 Docked ligands
88 ligands of Boehm, Stuerzebecher, Klebe (JMC 1999,42:458) were docked
into the bovine trypsin model. 38 ligands of the best ranked docking
solutions were selected manually. For these 38 ligands the interaction
energies were calculated and the Ki values were predicted by the
COMBINE model of bovine trypsin.docked_trypsin-klebe.sdf )gold_protein.mol2 active_atoms.pdb External PLS
predictions for
/home/henricsn/combine2go/data/trypsin/dock_klebe/min/golpe/output.dat 1
Z01.1
Exper:
-10.5 Pred:( 1 ) -8.824
( 2 ) -8.41 ( 3 ) -8.637 ( 4
) -9.14 ( 5 ) -9.611 2
Z02.2
Exper:
-8.568 Pred:( 1 ) -9.172 ( 2
) -9.634 ( 3 ) -10.08 ( 4 )
-10.53 ( 5 ) -11.39 3
Z03.3
Exper:
-8.368 Pred:( 1 ) -10.3
( 2 ) -10.35 ( 3 ) -10.52 ( 4 )
-10.44 ( 5 ) -10.83 4
Z04.4
Exper:
-8.978 Pred:( 1 ) -9.256 ( 2
) -9.067 ( 3 ) -9.034 ( 4 )
-9.588 ( 5 ) -10.18 5
Z05.5
Exper:
-9.105 Pred:( 1 ) -8.939 ( 2
) -8.756 ( 3 ) -9.074 ( 4 )
-9.614 ( 5 ) -9.997 6
Z06.6
Exper:
-8.125 Pred:( 1 ) -8.938 ( 2
) -8.545 ( 3 ) -8.484 ( 4 )
-8.902 ( 5 ) -9.151 7
Z07.7
Exper:
-7.36 Pred:( 1 )
-9.1 ( 2 ) -9.63
( 3 ) -9.96 ( 4 ) -10.49 ( 5
) -11.43 8
Z08.8
Exper:
-8.837 Pred:( 1 ) -9.476 ( 2
) -9.258 ( 3 ) -9.476 ( 4 )
-9.827 ( 5 ) -10.25 9
Z09.9
Exper:
-8.328 Pred:( 1 ) -8.769 ( 2
) -8.42 ( 3 ) -7.838 ( 4 )
-7.803 ( 5 ) -8.101 10
Z10.10
Exper:
-7.982 Pred:( 1 ) -10.88 ( 2
) -11.26 ( 3 ) -11.58 ( 4 )
-11.78 ( 5 ) -12.54 11
Z11.11
Exper:
-9.134 Pred:( 1 ) -8.873 ( 2
) -8.344 ( 3 ) -8.254 ( 4 )
-8.821 ( 5 ) -9.241 12
Z12.12
Exper:
-8.738 Pred:( 1 ) -9.249 ( 2
) -8.927 ( 3 ) -9.2 ( 4
) -9.72 ( 5 ) -10.38 13
Z13.13
Exper:
-8.455 Pred:( 1 ) -8.764 ( 2
) -8.777 ( 3 ) -8.586 ( 4 )
-9.127 ( 5 ) -9.774 14
Z14.14
Exper:
-8.073 Pred:( 1 ) -10.05 ( 2
) -9.703 ( 3 ) -9.005 ( 4 )
-8.663 ( 5 ) -9.557 15
Z15.15
Exper:
-8.073 Pred:( 1 ) -9.153 ( 2
) -8.75 ( 3 ) -8.781 ( 4 )
-9.202 ( 5 ) -9.53 16
Z16.16
Exper:
-9.078 Pred:( 1 ) -9.059 ( 2
) -8.658 ( 3 ) -8.851 ( 4 )
-9.231 ( 5 ) -9.319 17
Z17.17
Exper:
-8.504 Pred:( 1 ) -9.018 ( 2
) -8.915 ( 3 ) -8.974 ( 4 )
-9.486 ( 5 ) -10.33 18
Z18.18
Exper:
-8.667 Pred:( 1 ) -9.07
( 2 ) -8.905 ( 3 ) -9.09 ( 4
) -9.639 ( 5 ) -10.29 19
Z19.19
Exper:
-6.618 Pred:( 1 ) -9.607 ( 2
) -8.44 ( 3 ) -8.063 ( 4 )
-7.792 ( 5 ) -8.197 20
Z20.20
Exper:
-6.539 Pred:( 1 ) -10.4
( 2 ) -10.34 ( 3 ) -9.807 ( 4 )
-9.83 ( 5 ) -11.19 21
Z21.21
Exper:
-6.81 Pred:( 1 ) -9.956
( 2 ) -9.899 ( 3 ) -10.21 ( 4 )
-10.15 ( 5 ) -10.15 22
Z22.22
Exper:
-6.275 Pred:( 1 ) -10.87 ( 2
) -10.49 ( 3 ) -10.65 ( 4 )
-10.91 ( 5 ) -11.66 23
Z23.23
Exper:
-6.539 Pred:( 1 ) -9.101 ( 2
) -8.961 ( 3 ) -9.147 ( 4 )
-9.617 ( 5 ) -10.11 24
Z24.24
Exper:
-7.663 Pred:( 1 ) -10.27 ( 2
) -11.01 ( 3 ) -11.18 ( 4 )
-11.67 ( 5 ) -12.4 25
Z25.25
Exper:
-5.255 Pred:( 1 ) -9.846 ( 2
) -9.072 ( 3 ) -9.152 ( 4 )
-9.512 ( 5 ) -9.954 26
Z26.26
Exper:
-6.187 Pred:( 1 ) -9.062 ( 2
) -8.694 ( 3 ) -8.328 ( 4 )
-8.496 ( 5 ) -8.479 27
Z27.27
Exper:
-8.455 Pred:( 1 ) -10.32 ( 2
) -9.552 ( 3 ) -9.218 ( 4 )
-9.685 ( 5 ) -10.06 28
Z28.28
Exper:
-6.148 Pred:( 1 ) -9.368 ( 2
) -9.441 ( 3 ) -8.969 ( 4 )
-9.303 ( 5 ) -10.82 29
Z29.29
Exper:
-8.978 Pred:( 1 ) -10.65 ( 2
) -10.43 ( 3 ) -10.6 ( 4 )
-10.89 ( 5 ) -11.83 30
Z30.30
Exper:
-8.474 Pred:( 1 ) -10.2
( 2 ) -9.638 ( 3 ) -9.725 ( 4 )
-9.684 ( 5 ) -9.752 31
Z31.31
Exper:
-8.025 Pred:( 1 )
-8.6 ( 2 ) -8.499 ( 3 )
-8.809 ( 4 ) -9.238 ( 5 )
-9.591 32
Z32.32
Exper:
-8.667 Pred:( 1 ) -9.284 ( 2
) -9.059 ( 3 ) -9.277 ( 4 )
-9.843 ( 5 ) -10.36 33
Z33.33
Exper:
-8.384 Pred:( 1 ) -9.436 ( 2
) -8.705 ( 3 ) -8.448 ( 4 )
-8.671 ( 5 ) -9.059 34
Z34.34
Exper:
-8.193 Pred:( 1 ) -8.553 ( 2
) -8.42 ( 3 ) -8.141 ( 4 )
-8.115 ( 5 ) -8.493 35
Z35.35
Exper:
-9.266 Pred:( 1 ) -10.6
( 2 ) -10.15 ( 3 ) -9.973 ( 4 )
-10.18 ( 5 ) -10.56 36
Z36.36
Exper:
-10.41 Pred:( 1 ) -9.235 ( 2
) -8.732 ( 3 ) -8.789 ( 4 )
-9.261 ( 5 ) -9.704 37
Z37.37
Exper:
-6.251 Pred:( 1 ) -9.95
( 2 ) -9.865 ( 3 ) -9.78 ( 4
) -10.29 ( 5 ) -10.65 38
Z38.38
Exper:
-5.913 Pred:( 1 ) -8.934 ( 2
) -8.287 ( 3 ) -7.412 ( 4 )
-7.721 ( 5 ) -8.49
Y_1 Components SDEP (external)
0 1.5671
1 2.1194
2 1.9963
3 1.9713
4 2.1580
5 2.6521 Privacy Imprint