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| Voit E. — Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists |
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| Предметный указатель |
Degradation in GMA form 265 267 355 362 448
Degradation in S-system form 265 267 277 351 362 363 448 461
Degradation in splitting reactions 90
Degradation of proteins 294 314 315—316
Degradation of purine 330
Degradation of pyruvate 457 461
Degradation of SAM 342 343
Degradation of succinate 188 305 451
Degradation of xanthine 355 360 363
Degradation processes 26 31 45 49 53 54 72 79 135 265 312
Degradation product 94
Degradation speed 45 52 57 75 164 240
Degradation, activation of 220 214
Degradation, adenine 346
Degradation, adenylates 330 356
Degradation, ADP 458
Degradation, aggregation of terms 265 267 272 448
Degradation, approximation of 59
Degradation, ATP 267—268 292 458
Degradation, buffering and 135
Degradation, DNA/RNA 56 346 351
Degradation, drugs 133
Degradation, ethanol 291
Degradation, flux 85 191
Degradation, fructose-6-phosphate 109 273—275
Degradation, glucose-6-phosphate 167—171 271—273 278 391
Degradation, glycogen 365 398
Degradation, inhibition 52 195 206 220 346 355
Degradation, isocitrate 165—167 322
Degradation, kinetic order 55 127 169 304 339 342 448
Degradation, metabolite 77 78
Degradation, phosphoenolpyruvate 262
Degradation, power-law rate law 167 168 451
Degradation, PRPP 12 334 335 349 351 362 363 461
Degradation, rate constants 50 123 267
Degradation, substrate 46 75 90
Degradation, term 50 51 55 67—68 70 77 87 88 108 119 135 168 317 335 360 457 461
Degrees of freedom 191 411
Delay equations 131
Delbarre, E 364 472
Delgado, J. 157 472
Demand theory 400 401
Deoxyadenosine (dAdo) 331 333 336 347 352
Deoxyadenosine diphosphate (dADP) 333 336 347 352
Deoxyadenosine monophosphate (dAMP) 333 336 347 348 352
Deoxyadenosine triphosphate (dATP) 333 336 347 348 352
Deoxyguanosine (dGuo) 331 333 336 347 353
Deoxyguanosine diphosphate (dGDP) 333 336 347 352
Deoxyguanosine monophosphate (dGMP) 333 336 347 348 352
Deoxyguanosine triphosphate (dGTP) 333 336 347 348 352
Deoxyinosine (dINO) 331 333 347
Deoxynucleotides 327 331
dependent variables 262—264 268 275 284 285 291 306 307 311 324 332 337 343 346 362 368 376 379 381 384 385 387 388 391 392 397 398 406 409 415 416 421—423 434 445 457 464
Dependent variables for branched pathways 82 112 141 177 178
Dependent variables for linear pathways 115
Dependent variables for productivity assessment 131—133
Dependent variables in cascades 86 180—182
Dependent variables in glycolysis 28—29 370 377—378
Dependent variables in zymogen activation 29 30
Dependent variables intermediate 22 131
Dependent variables, bolus experiments 108
Dependent variables, change in 39 41—49 51 56 105 108 109 121 122—123 246 377—378
Dependent variables, closed vs. open systems 93 94
Dependent variables, conserved masses and 90
dependent variables, defined 21
Dependent variables, differential equations 48
Dependent variables, enumeration of 76—77
Dependent variables, equation construction 48 52 54 77—79
Dependent variables, flux sensitivity 244
Dependent variables, independent variables distinguished 22 23
Dependent variables, logarithmic gain 224 225 227—231
Dependent variables, mapping 24 27 28 29—30 31
Dependent variables, notation 59
Dependent variables, parameter estimation 122—123 143 144 172 173 175 177 178 180—182 190
Dependent variables, phase-plane plots 110 111
Dependent variables, rate constant sensitivities 237
Dependent variables, reduced set of 257 258
Dependent variables, replacement with independent variable 128
Dependent variables, S-system 193 196 197 198 205 206 209 212 217 220
Dependent variables, sensitivity analysis 224 225 227—231 237 244 246 247 249 250 252—254 257 258
Dependent variables, steady-state values 119 120 121 122 123 124 193 196 197 198 205 206 209 212 217 220
Dependent variables, sum of 102
Dependent variables, value 22 52 102 119 120 121 122 123 124 127
DeRisi, J.L. 17 18 472 479
derivatives 38 42 44 56 65 110 136 138 147 159 161 165 189 196 198 217 220 25 227 230 234 235 242 244 251 253 254 255 258 260 287 328 406 418 419 420 451
Derivatives logarithmic 156 191 252 450
Derivatives partial 88 89 166 167 170 225 230 241 304 318 394 414 424 425 440 460 461
Derivatives, slopes instead of 174—184
Design principles 3—4 7
design process 8 9 16 17 262 395—396
Determinants 193 200—204 206—210 213 216 218 220 239 382 414 435 437 440 453
Determinants, expansion 211 214 432 434 436 442 467—468
Determinants, linear algebra 430—434
Determinants, minors 433 438
Determinants, total 252—255
Determinism 3
Deterministic 1 410
Detoxification 136
Developmental time scales 6
Diabetes 6 366
Diagnostic analysis 297
Dichotomous effect 12
DICTIONARY 20 28 29 298
Dictyostelium discoideum 129 165—167 171—172 188 223 293—325
Didactic pathway 115 127 176 256 405
Differential equations 8 42—48 51 56—59 65—68 75 77 94 99 101—103 107 123 127 135 137 138 172—175 178 193—195 203 209 220 224 250 256 264 295 297 350 357 363 389 404 406 407 409 410 417 444 445 449 451 458
Differential, total 155 424
Differentiation 140 144 159 166 190 193 219 229 233 236 241 243—245 247 248 251 257 270 291 294 295 297 315 392 418 425 446—448 455 see
Digitonin technique 151 152
Dihydrolipoyl dehydrogenase 300
Dihydrolipoyl transacetylase 300
Dihydroxyadenine 364
Directed connections 64
Directed graph 61 63
Diribonucleotide reductase (DRNR) 334 348
Disease pattern 327 328 396
Disease state 138 193 356 360
Disease, metabolic 345
Dissociation 39
distribution 46 139 294 314 315 327 338 410 411 412
Divergence branch point 25 26 27 77 95 267 323—324
Diverging pathway 95 267 288
DNA 63 145 327 330 347 348 352 353
DNA Data Bank of Japan (DDBJ) 18
DNA, chips 17 18
DNA, degradation 56 346 351
DNA, microarrays 17—18
DNA, model 6
DNA, recombinant 287—288
DNA, sequencing 8 18
DNA, synthesis and degradation 56
Domach, M.M. 284 480
Domain 151 415
Donachies, W. 149 473
Dong, H. 18 171 472 493
Doran, P.M. 260 274 473
dot notation 42 44
Double modulation 157—158
Double-headed arrow 25 26 27 28—29 346
Double-tailed arrow 27 28—29 87 346
Dougherty, B.A. 8 473
Dove, W. 8 470
Drosophilia melanogaster 16
Drugs, degradation of 133
Drugs, inter-individual variability of response to 9 412
Drugs, intervention simulation 141 357 360—361
Drugs, metabolism 133 134 137 141
Drugs, resistance 141
Drugs, screening/testing 1 7 8 327 362 399
Drugs, uricosuric 367—368 462
| Duggan, D J. 18 473
Dujon, B. 8 9 475
Dunhill, P. 285 286 396 408 483
Dykhuizen, D.E. 149 473
dynamic data 143
Dynamic data, branched pathway 176—179
Dynamic data, cascades 179—184
Dynamic data, direct estimation from 173—174
Dynamic data, parameter estimation from 172—185
Dynamic data, regression 173—174
Dynamic data, slopes instead of derivatives 174—184
Dynamic response 80 97 112 114 142 143 182 283 325 330 364 397
Dynamical exploration 342
Dynamical solution 84 85 119 120 122 124 126 280 353 361 448 456
Dynamics 60 61 68 78 90 94 103 128 132 140 141 144 146 155 171 172 196 198 199 200 219 221 260 262—264 291 292 327 330 331 333 340 342 343 346 351 357 389 398 403 406 444 445 448 449 452 453 457 461
Dynamics in S-systems 54—55 282—283
Dynamics of biochemical systems 41—49 56 282—283
Dynamics of components 5
Dynamics of networks 63
Dynamics of organisms 5
Dynamics of Petri nets 64
Dynamics of transient responses 105—107
Dynamics, anaerobic fermentation pathway model 282—283
Dynamics, ATP 275—277
Dynamics, bolus experiments 107—108
Dynamics, closed vs. open systems 93
Dynamics, computer simulation 105—119 125
Dynamics, controlled comparisons 114—118
Dynamics, enzyme-catalyzed reactions 43—44 64
Dynamics, feedback 111—115
Dynamics, modification of system characteristics 109—110
Dynamics, molecular level 5 38 39
Dynamics, pathway 38 111—115
Dynamics, persistant changes 108—109
Dynamics, phase-plane plots 110—111
Dynamics, simple pathway with surprise 115—119
Dynamics, steady state 124 130—131
Dynamics, time scale and 6
Dzubow, L. 38 474
Easterby, J.S. 216 232 389 473
Eblen, S.T. 171 486
EC Enzyme Database 15
EcoCyc 16
Ecosystems 11 400
Edelstein-Keshet, L. 212 473
Educated guess 144 345
Edwards, N.L. 359 473
Efficiency 8 19 66 67 86 137 174 216 232 314 323 402 406 419
Efflux 70 73 91 133 144 164 185 194 216 217 232 267 303 305 318 319 331 445 447
Eigenvalues 124—126 209—213 216 280 289 307 309—311 319 320 324 375 376 379 380 402 448
Eigenvalues, complex conjugate 340
Eigenvector 209
Eiglmeier, K. 8 471
Einstein's theory of relativity 37
Einstein, Albert 3
EKG 125
Elastase 29—30
Elasticities 148 153
Electric circuit 48
Elemental chemical kinetics 44 46 53 55
Elion, G.B. 361 473
EMP Enzymology Database 15
Enabling transitions 64
End-product inhibition 80—81 111 122
Endonuclease 346
Energy chemical 14 28
Energy, storage 328 365
Enteropeptidase 30 31
Environment 5 8 24 92 103 109 117 123 222 294 401 402 407 411 412
Environmental Protection Agency (EPA USA) 140 473
Enzyme Reaction Mechanism (ERM) database 16
Enzyme(s) 7 11 16 23 25 31 32 40—42 49 59 62 64 68 105 125 135 138 144 146 150 155 157 159 160 163 165 168 233 246 262 264 268 274 278 284 286 289 295—298 300 305 312 314 315 322—324 327—329 334 340 341 343 344 348 363 368—370 395 396 399 405 407 421 447
Enzyme(s) in models 38
Enzyme(s) overexpressed 290
Enzyme(s), activity 17 122 139 140 148 149 170 188 222 271 273 276 287 310 311 313 320 355—360 360 372 373 375 443
Enzyme(s), affinity 109
Enzyme(s), binding 39
Enzyme(s), bound form 21 90 171
Enzyme(s), concentration constraints 287—288
Enzyme(s), databases 15
Enzyme(s), deficiency 356 443
Enzyme(s), dissociation 39
Enzyme(s), free form 21 90
Enzyme(s), graphical representation 20—21 27
Enzyme(s), polymorphisms 9 17
Enzyme(s), replacement 362
Enzyme(s), scaffold 171
Enzyme(s), unbound form 90 171
Enzyme-catalyzed processes 11 12 25 38 43—44 53 56 64 298 406
Enzyme-enzyme interaction 246
Equation construction, bimolecular reactions 87 88—89
Equation construction, branch-point constraints 82—86 89
Equation construction, branched pathways 77 81—86 89
Equation construction, cascades 86—87
Equation construction, closed systems 93—94
Equation construction, conserved masses 90—91
Equation construction, constraint derivation 87—91
Equation construction, dependent variables 48 52 54 77—78
Equation construction, end-product inhibition 80—81
Equation construction, enumeration of variables 76—77
Equation construction, examples 78—87
Equation construction, exercises 94—96
Equation construction, linear pathways 78—81
Equation construction, open systems 93—94
Equation construction, precursor-product constraints 79—80
Equation construction, purine metabolism model 332—338
Equation construction, reversible pathways 91—93
Equation construction, S-system representations 70 74 76 77 78—80 82—84 92 94 99—103 277—278 338—340 375
Equation construction, stoichiometric constraints 90
Equation construction, tricarboxylic acid cycle 298—306
Equilibrium 163 262 263 264 271 272 434
Equilibrium constant 22 162 169 323 325 367 368 372 373 374 396 398
Equilibrium, thermodynamic 3 92 163 405 462
EQUIVALENCE 79 90 232 246 316 317 379 407 408 461
Equivalence, external 114—115
Equivalent 43 57 66 73 79 88 89 91 93 94 130 137 147 148 184 185 204 210 225 229 248 255 267 277 306 319 371 378 379 382 389 391 397 401 404 410 422 447 449 461
Equivalent, systems 115
Erfle, J.D. 297 484
Ericson, A. 146 149 150 472
Error structure 148
Escherichia coli 3 16 62 293 400 401
Essence of the system 40
Essentially irreversible reaction 25 28 91 168 298 300 304 329 331 367
ESSYNS 67 407
Estimation 92 222 265 268 269 291 307 328 333 340 351 365 391 393 395 396 397 398 404 421 426 427 see
Ethanol 260 261 262 263 267 273 275 281 285 286 288 289 290 291
Ethics 8
Eukaryotes 8
Euler's algorithm 66—67 74
European Bioinformatics Institute Macromolecular Structure Database (EBI/MSD) 18
European Molecular Biology Laboratory (EMBL) database 18
Evolutionary 6 160 222
Exact analogues 137—138
Exact model 50
Exact representation 418
Exhaustive exploration 139 174
Exogenous influences 119 125 126
Exogenous products 285
Exogenous substrate 41 93 94
Exogenous supply 93 94 109 122 187 354
Exogenous, bolus 103 108 109 122 377 397
Exonuclease 346
expansion 54 131 202 203 226 284 296 366
Expansion of determinants 211 214 432 434 436 442 467—468
ExPASy Molecular Biology Server 16 19
Exponential function 44 53 65—66 66 134 137 195 381 439 466
Expression profile 9 18
External equivalence 114—115 316 319 379 407 408
External variables 22
Extrapolation 126 149 171 226 403
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