all 34 urokinase structures with alternative conformations --------------------------------------------------------------- --------------------------------------------------------------- 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 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 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 --------------------------------------------------------------- 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 --------------------------------------------------------------- 6 PLS 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 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 --------------------------------------------------------------- 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 --------------------------------------------------------------- Partial Least Squares (PLS) 34 objects 105 X-var 1 Y-var Y1 components XVarExp XAccum SDEC r2 0 0.0000 0.0000 6.1213 0.0000 1 87.3947 87.3947 5.4249 0.2146 2 5.0456 92.4403 4.1314 0.5445 3 1.5070 93.9473 3.3773 0.6956 4 3.4153 97.3625 3.2114 0.7248 5 0.4637 97.8262 2.2083 0.8698 6 0.4360 98.2623 1.7683 0.9165 7 0.6310 98.8933 1.6141 0.9305 8 0.1520 99.0452 1.3048 0.9546 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 4.0489 - 0.5625 4 4.0128 - 0.5703 5 3.6266 - 0.6490 6 3.3337 - 0.7034 7 3.3928 - 0.6928 8 3.6329 - 0.6478 --------------------------------------------------------------- *** 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 0.1 Regression coefficients of the 1-dimensional model 0 -36.83 Regression coefficients of the 2-dimensional model 0 -42.22 30 +0.4404 31 +0.2545 46 -0.2206 47 +0.8 48 +0.1179 50 +0.1598 193 +0.3297 194 -0.1278 195 -0.3934 197 -0.1075 198 +0.4981 219 +0.2136 221 +0.1201 222 +0.1163 229 +0.1016 230 +0.1835 231 +0.1633 246 +0.4509 265 +0.1039 267 +0.13 295 -0.3312 339 +0.7758 342 -0.6772 387 +0.5133 431 -0.133 437 +0.2379 438 -1.156 441 -0.4563 442 -0.5672 461 -0.1153 462 +0.1746 464 -0.1759 465 +0.3398 466 +0.2885 467 -0.1287 471 -0.1359 472 +0.2481 474 +0.2704 475 +0.1172 476 -0.1561 Regression coefficients of the 3-dimensional model 0 -47.51 30 +0.5744 31 +0.3509 46 -0.2425 47 +1.017 48 +0.1561 50 +0.2149 193 +0.3427 194 -0.1318 195 -0.4599 197 -0.1104 198 +0.5084 219 +0.2657 220 +0.1204 222 +0.1614 229 +0.1056 230 +0.1963 231 +0.1739 246 +0.473 265 +0.1099 267 +0.1647 295 -0.3956 339 +0.8296 342 -0.7378 387 +0.5752 431 -0.1426 438 -0.9844 441 -0.6069 442 -0.6159 443 -0.2808 461 -0.1337 462 +0.2537 464 -0.1566 465 +0.3428 466 +0.4718 467 -0.1005 471 -0.1407 472 +0.2746 474 +0.3148 475 +0.1198 476 -0.1856 Regression coefficients of the 4-dimensional model 0 -36.1 29 +0.1373 30 +0.8444 31 +0.5791 46 -0.2284 47 +1.489 48 +0.2369 49 +0.1119 50 +0.3326 150 +0.1446 193 +0.3636 194 -0.1334 195 -0.5413 197 -0.1005 198 +0.3827 219 +0.4096 220 +0.2162 222 +0.2838 229 +0.1098 230 +0.2141 231 +0.1828 246 +0.4854 265 +0.1059 267 +0.2287 295 -0.5313 339 +0.873 342 -0.8106 387 +0.6822 431 -0.143 438 -0.5317 441 -0.765 442 -0.6984 443 -0.22 461 -0.1727 462 +0.4515 464 -0.12 465 +0.3376 466 +0.9581 471 -0.1343 472 +0.3394 474 +0.4308 475 +0.131 476 -0.2562 Regression coefficients of the 5-dimensional model 0 -19.4 20 +0.1211 29 +0.2254 30 +1.296 31 +0.9877 46 -0.1831 47 +2.254 48 +0.3778 49 +0.1793 50 +0.5497 51 +0.1139 57 +0.1118 145 +0.1109 150 +0.2168 193 +0.5121 195 -0.4972 196 -0.1474 198 -0.2027 216 -0.1894 219 +0.7352 220 +0.4398 221 -0.1264 222 +0.5651 228 +0.1153 230 +0.1994 231 +0.1457 246 +0.3728 267 +0.3302 295 -0.7575 298 +0.1346 339 +0.6668 342 -0.7026 387 +0.7521 390 +0.1123 438 -0.4571 441 -1.041 442 -0.695 443 -0.2524 461 -0.2303 462 +0.8566 465 +0.205 466 +2.092 470 -0.1881 472 +0.3738 474 +0.4854 476 -0.3643 Regression coefficients of the 6-dimensional model 0 -15.33 20 +0.1333 29 +0.2483 30 +1.385 31 +1.095 47 +2.426 48 +0.4127 49 +0.1958 50 +0.6042 51 +0.1269 57 +0.1222 94 +0.1009 145 +0.1374 150 +0.24 193 +0.5739 195 -0.2289 196 -0.1727 198 -0.3244 216 -0.2207 219 +0.8577 220 +0.5392 221 -0.2299 222 +0.6947 228 +0.1247 230 +0.2137 231 +0.1499 246 +0.4286 267 +0.3535 295 -0.8491 298 +0.1545 334 +0.1067 339 +0.7112 342 -0.7095 387 +0.9146 390 +0.1149 431 -0.1146 438 -0.4141 441 -0.7184 442 -0.8241 443 -0.3776 461 -0.2557 462 +1.019 465 +0.2275 466 +2.519 467 +0.1585 470 -0.2299 472 +0.4346 474 +0.5029 476 -0.4023 --------------------------------------------------------------- list 0.2 Regression coefficients of the 1-dimensional model 0 -36.83 Regression coefficients of the 2-dimensional model 0 -42.22 30 +0.4404 31 +0.2545 46 -0.2206 47 +0.8 193 +0.3297 195 -0.3934 198 +0.4981 219 +0.2136 246 +0.4509 295 -0.3312 339 +0.7758 342 -0.6772 387 +0.5133 437 +0.2379 438 -1.156 441 -0.4563 442 -0.5672 465 +0.3398 466 +0.2885 472 +0.2481 474 +0.2704 Regression coefficients of the 3-dimensional model 0 -47.51 30 +0.5744 31 +0.3509 46 -0.2425 47 +1.017 50 +0.2149 193 +0.3427 195 -0.4599 198 +0.5084 219 +0.2657 246 +0.473 295 -0.3956 339 +0.8296 342 -0.7378 387 +0.5752 438 -0.9844 441 -0.6069 442 -0.6159 443 -0.2808 462 +0.2537 465 +0.3428 466 +0.4718 472 +0.2746 474 +0.3148 Regression coefficients of the 4-dimensional model 0 -36.1 30 +0.8444 31 +0.5791 46 -0.2284 47 +1.489 48 +0.2369 50 +0.3326 193 +0.3636 195 -0.5413 198 +0.3827 219 +0.4096 220 +0.2162 222 +0.2838 230 +0.2141 246 +0.4854 267 +0.2287 295 -0.5313 339 +0.873 342 -0.8106 387 +0.6822 438 -0.5317 441 -0.765 442 -0.6984 443 -0.22 462 +0.4515 465 +0.3376 466 +0.9581 472 +0.3394 474 +0.4308 476 -0.2562 Regression coefficients of the 5-dimensional model 0 -19.4 29 +0.2254 30 +1.296 31 +0.9877 47 +2.254 48 +0.3778 50 +0.5497 150 +0.2168 193 +0.5121 195 -0.4972 198 -0.2027 219 +0.7352 220 +0.4398 222 +0.5651 246 +0.3728 267 +0.3302 295 -0.7575 339 +0.6668 342 -0.7026 387 +0.7521 438 -0.4571 441 -1.041 442 -0.695 443 -0.2524 461 -0.2303 462 +0.8566 465 +0.205 466 +2.092 472 +0.3738 474 +0.4854 476 -0.3643 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 ---------------------------------------------------------------