uPA-trypsin

Combine analysis: uPA-trypsin_310105 (31.01.2005)

urokinase (uPA)

CRA	trypsin	trypsin	uPA	uPA
10656	A01	1o2k
18607	A02	1o36
23653	A03	1o38*
8696	A04	1o3g*	A04	1o5a (115)
17693	A05	1o30
10972	A06	1o2p
16847	A08	1o2x*
1801	A09	1o33
9678	A10	1o3l
10991	A11	1o2q
1144	A12	1gi2	A12	1gi8 (101)
6669	A13	1gi5	A13	1gi9 (121)
7806	A14	1o3c	A14	1gjb (122/123), 1gjc (116/117)
10655			A15	1o3p (124/125)
10950	A16	1o2o	A16	1gj8 (126)
11092	A17	1o2r	A17	1gj9 (127-130), 1o5c (103/104)
10302	A18	1gj6	A18	1gj7 (131/132)
6860			A19	1c5x (113/114), 1c5w (111/112), 1o5b (109/110)
benzamidine			A20	1c5z (120), 1f5k (133)
7538			A21	1c5y (118/119)
10273			A22	1gi7 (107/108)
11421			A23	1gjd (106)
7136			A24	1gja (105)
AGB			A25	1ejn (102)
amiloride			A26	1f5l (134)
#used (unique)	13	13	16	16
#used + altconf		15		34

red: ligands or parts of it not well defined in electron density map
orange: no electron density map available
blue: chemical structure of ligand of corrected

*not used:
A03/1o38: defined part as A14/1o3c
A04/1o3g: ED for ligand unclear
A08/1o2x: aromatic ring with bromide and other substituents not defined in ED

SDF file (uPA-trypsin_310105.sdf)

convert.sh (*pdb *.modif.pdb, *.ligand.pdb, *.log.pdb)

xleap.sh (*.modif.pdb, *.ligand.pdb  *.min.pdb, *.cor, *.top, *.prep, *.parm)

prep_interaction.sh (*.min.pdb  *.pdb.cut)

creating an alignment with STRAP (STRAP)
http://projects.villa-bosch.de/mcm/projects/tassfun/combine/results/uPA-trypsin_030205/uPA-align.html
cut all the pdb files *.pdb.cut to the same sequence length

calc_interaction.sh (*.cut.pdb  *.xcut.pdb, *.outa)

creating anal (amber7) output file

golpe (*.outa  *.dat)

GOLPE 4.5

import interactions/AMBER
AMBER ANAL files: ###.outa (uPA.outa.tar.gz)
GOLPE new file: uPA1.dat
Number of the Ligand: 246

Type varibles/Name
mv dat.VarNames uPA1.dat.VarNames

import activity.txt (skip first column)

A12 1gi8_101 -29.8
A25 1ejn_102 -32.1
A17 1o5c.192A_103 -42.7
A17 1o5c.192B_104 -42.7
A24 1gja_105 -30.9
A23 1gjd_106 -29.8
A22 1gi7.192B_107 -25.7
A22 1gi7.192A_108 -25.7
A19 1o5b.192A_109 -38.1
A19 1o5b.192B_110 -38.1
A19 1c5w.192B_111 -38.1
A19 1c5w.192A_112 -38.1
A19 1c5x.192B_113 -38.1
A19 1c5x.192A_114 -38.1
A04 1o5a_115 -40.8
A14 1gjc.192A_116 -36.4
A14 1gjc.192B_117 -36.4
A21 1c5y.A21A_118 -24.0 
A21 1c5y.A21B_119 -24.0
A20 1c5z_120 -30.3
A13 1gi9_121 -29.8
A14 1gjb.192B_122 -36.4
A14 1gjb.192A_123 -36.4
A15 1o3p.192B_124 -38.0
A15 1o3p.192A_125 -38.0
A16 1gj8_126 -39.7
A17 1gj9.192A_A17_A_127 -42.7
A17 1gj9.192A_A17_B_128 -42.7
A17 1gj9.192B_A17_A_129 -42.7
A17 1gj9.192B_A17_B_130 -42.7
A18 1gj7.192B_131 -45.4
A18 1gj7.192A_132 -45.4
A20 1f5k_133 -30.3
A20 1f5l_134 -30.1

log-file (edited)

Data file : /home/henricsn/Combine/tassfun/uPA-trypsin_030205/uPA/uPA3.dat
Comment : Imported from AMBER
Loading :
1 1011gi8
2 1021ejn
3 1031o5c
4 1041o5c
5 1051gja
6 1061gjd
7 1071gi7
8 1081gi7
9 1091o5b
10 1101o5b
11 1111c5w
12 1121c5w
13 1131c5x
14 1141c5x
15 1151o5a
16 1161gjc
17 1171gjc
18 1181c5y
19 1191c5y
20 1201c5z
21 1211gi9
22 1221gjb
23 1231gjb
24 1241o3p
25 1251o3p
26 1261gj8
27 1271gj9
28 1281gj9
29 1291gj9
30 1301gj9
31 1311gj7
32 1321gj7
33 1331f5k
34 1341f5l

Number of variables = 491
Number of experiments = 34
Number of X-variables = 490 , Y-variables = 1
Active X-variables (SS 1.0E-7) = 210
Active Y-variables (SS 1.0E-7) = 1
---------------------------------------------------------------
Principal Component Analysis (PCA) 34 objects 210 X-var
components XVarExp XAccum
1 87.7807 87.7807
2 4.9354 92.7161
3 3.6448 96.3609
4 1.3030 97.6639
5 0.7957 98.4596

PCA Rank Validation - using 4 random groups
components PRESS Seps R
1 4.1132e+03 1.9150e+04 0.2148
2 7.8621e+03 2.2645e+03 3.4720
3 7.9335e+02 1.3050e+03 0.6079
4 9.9534e+02 6.2965e+02 1.5808
5 5.6539e+02 3.8993e+02 1.4500
- 3 PCA
---------------------------------------------------------------
uPA3_pca-sco_1-2.xy
uPA3_pca-sco_1-3.xy
uPA3_pca-sco_2-3.xy
---------------------------------------------------------------
Partial Least Squares (PLS) 34 objects 210 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.1213 0.0000
1 87.3922 87.3922 5.4248 0.2146
2 5.0459 92.4381 4.1313 0.5445
3 1.5073 93.9454 3.3771 0.6956
4 3.4154 97.3608 3.2111 0.7248
5 0.4634 97.8242 2.2082 0.8699
6 0.4363 98.2605 1.7684 0.9165
7 0.6309 98.8914 1.6139 0.9305
8 0.1520 99.0434 1.3037 0.9546
9 0.2048 99.2482 1.1020 0.9676
10 0.1235 99.3717 0.9649 0.9752

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.3068 - -0.0615
1 5.7763 - 0.1095
2 4.6504 - 0.4228
3 4.0488 - 0.5625
4 4.0127 - 0.5703
5 3.6266 - 0.6490
6 3.3347 - 0.7032
7 3.3935 - 0.6927
8 3.6351 - 0.6473
9 3.6732 - 0.6399
10 3.8364 - 0.6072
---------------------------------------------------------------
uPA3_exp-pred_6PC.xy
---------------------------------------------------------------
Deleted unselected vars. (D-Optimal)
1 : 210 - 105 Comp.=6 , Tue Feb 15 16:55:58 2005
Active X-variables after VAR. SELECT. = 105
---------------------------------------------------------------
*** 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 : 105 - 98 Comp.=6 , Tue Feb 15 17:36:22 2005
Active X-variables after VAR. SELECT. = 98
---------------------------------------------------------------
Partial Least Squares (PLS) 34 objects 98 X-var 1 Y-var
Y1 components XVarExp XAccum SDEC r2
0 0.0000 0.0000 6.1213 0.0000
1 89.6754 89.6754 5.6888 0.1363
2 0.7463 90.4218 3.3908 0.6932
3 3.4620 93.8838 3.1476 0.7356
4 2.7337 96.6174 2.7528 0.7978
5 1.0363 97.6538 2.0021 0.8930
6 0.8929 98.5467 1.7341 0.9197
7 0.2906 98.8373 1.4676 0.9425
8 0.3462 99.1834 1.3660 0.9502
9 0.1962 99.3796 1.1994 0.9616
10 0.0848 99.4645 0.9561 0.9756

PLS Model Validation - LOO
Y1 components SDEP SDEV(sdep) q2
0 6.3068 - -0.0615
1 6.0391 - 0.0267
2 5.1908 - 0.2809
3 3.9276 - 0.5883
4 3.9377 - 0.5862
5 3.1451 - 0.7360
6 2.6958 - 0.8061
7 2.5243 - 0.8299
8 2.7300 - 0.8011
---------------------------------------------------------------
uPA3_D-FFD_expr-pred_6PC.xy
uPA3_D-FFD_expr-pred_6PC.ps
---------------------------------------------------------------
list 0.2
Regression coefficients of the 6-dimensional model
0 -15.33
29 +0.2483 30 +1.385 31 +1.095 47 +2.426
48 +0.4127 50 +0.6042 150 +0.24 193 +0.5739
195 -0.2289 198 -0.3244 216 -0.2207 219 +0.8577
220 +0.5392 221 -0.2299 222 +0.6947 230 +0.2137
246 +0.4286 267 +0.3535 295 -0.8491 339 +0.7112
342 -0.7095 387 +0.9146 438 -0.4141 441 -0.7184
442 -0.8241 443 -0.3776 461 -0.2557 462 +1.019
465 +0.2275 466 +2.519 470 -0.2299 472 +0.4346
474 +0.5029 476 -0.4023
---------------------------------------------------------------
list 0.2 6-dimensional model
- images in pymol
---------------------------------------------------------------

trypsin

...COMBINE analysis still under construction.
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