Xu Y., Xu D., Liang J. — Computational Methods for Protein Structure Prediction & Modeling. Volume 1 :: Электронная библиотека попечительского совета мехмата МГУ

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Xu Y., Xu D., Liang J. — Computational Methods for Protein Structure Prediction & Modeling. Volume 1

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Название: Computational Methods for Protein Structure Prediction & Modeling. Volume 1

Авторы: Xu Y., Xu D., Liang J.

Язык:

Рубрика: Математика/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2007

Количество страниц: 406

Добавлена в каталог: 18.11.2012

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID

Предметный указатель

$C\alpha$ or $C\beta$       256
$\alpha$ -Lactalbumin      3 321
$\beta$ -helical      293 295—296 0
$\beta$ -sheet      28 131 135 137—138 141 209 222 225 259 282 285—286 289 291 293—297 299—303
3D-jury      16
3D-profile      7
Ab initio folding      9
Ab initio protein stincture prediction      9 11
Accessibility      7 19 50 74 90 239 266 286 288 291 325 334
Accessible topology      377 379—380 382
Additivity      110 291
Alanine dipeptide      48 55 57
Alignment sensitivity      319
Alignment tuning      326 338
Alpha complex      187 190 193
Alpha helix      326
Alpha shape      88—89 103 110 112 186—190 193 195—196
AMBER      2 45 50 53—58 332
Amyloid      280—297 305
Amyloid conformational states      284
Amyloid structure      282—285 289—290 294 305
Anfinsen’s theory of protein folding      1
Anti-cooperative, anti-cooperativity      122
Artificial evolution      5 327
Association rules      262 268
Atomic force microscopy      285
authors      126 139
Automated classification      149 166—167 171 174 176
Backbone      5 10 12—13 15 25 56 114 137 149 155 197 201 209 221 230
Bayesian Markov chain Monte Carlo      181 197
Beta pleated sheet      28 131 135 137—138 141 209 222 225 259 282 285—286 289 291 293—297 299—303
Beta strand      234
Blue Gene Project      9
Boltzmann assumption      74 76 108
Boltzmann distribution      74 76 93 108
Boundary surface      113—114 183—184
CAFASP      15
Cambridge structural database      51
CAPRI      15 103
CASP      12 14 16 25 238—239 268—269 337 347
CastP      191 193 198
CATH      22 126 139 156 167 176 201 269 380
CATH database      23 267
CE      155
Cedar      58
CHARMM      2 45 47 50 52—58 329 332 342
Circular’ dichroism      225 286
Class I force fields      48
Class II force fields      47 48
Cluster      110 129 135—137 240 335 368
CMAP      48 56 266
Coiled-coil      221 236—237
Coils      236—237 283 303
Colony energy      332—333 338 340—344
Compar ative modeling      2 3 5 13 22 28 29 320 322—323
COMPOSER      4 5 327
Composite model      326
Concave spherical surface      184 188
Condensed phase      47 49 51 55 58
Conformation sampling      102 322 329 335 336 342 344
Conformational energy      48 52 55 56 343
Conformational flee energy      337
Conformational searching      10 25 320
Connolly’s surface      183—184
Consensus alignment      157 175
Consensus evaluation      139 375
Consensus prediction      16 218 219 235 236 344
Conserved regions      4 296 321 327 328
Contact density      128—129 131 135—137 265
Contact map      149 255
Contact map error (CME)      257
Contact map prediction      255 262
Contact order (CO)      258—259 269
Contact potentials      74 109 256
Contact substitution matrix      271
Contact, residues      73
Contiguous, domain      129 134
Convex hull      95 185 191 192
Convex spherical surface      184
Cooperative, cooperativity      110 231
Correlated mutation      262—263 265—268 271—272
Coulomb ic interactions      45 47
Critical Assessment of Structure Prediction (CASP)      12 14—16 25 238—239 268—269 337 347
Cross-linking      288—289 329
Cross-p structure      293 295—296
Cryo — EM      27—28 181—182 285 292 359 363—365 370—371 374 377 382
Curved lineg segments      184
CVFF      58
DALI      22 151 154—156 161 164—165 167 169 171
Deconvolution method      366—367 370—371 373
DEE (Dead End Elimination)      13
Delaunay complex      186—187
Delaunay edge      89 185—186 192
Delaunay tetrahedrization      112 185—187 191—193 196 202
Delaunay triangulation      88 110 185 190 192—193
Density maps      27—28 225 359
DFIRE      87 111—112
Dihedral angle      47 52 55 73—74 329 377—378
Discontinuous molecular dynamics      303
Discrete flow      190—191
Discrete molecular' dynamics      303
DisEMBL      226 238
DISOPRED      226 239
Disordered region detection      224 243
DISPRO      226 239
Distance matrix      149 153 175 256—257
Distance matrix error (DME)      150 256
docking      12—13 15 24—26
Domain assignment      22—23
Domain, structural      129—130
Domain-domain interactions      22 24
DomainParser      22 133 137 139 141—142
Double dynamic programming      8 152 153
Drude oscillator      59
Drug design      59 323
Dynamic programming      7—8 152—153 155—156 159 197 219 236 324 335
Edge-flip      192
Effective eneigy      71 110 336 337
Effective resolution      373 384
Elastic scoring measure      154
Electr on microscopy      27 181 271 285 291 323
Electro density map      181 225 365
Electro static interactions      2 26 46 49 53 82 334
Electro static potential      82
Electron cryomicroscopy      27 359
Electron spin resonance      286
Electronegativity equilization methods      52
Electronic polarizability      52 59
Elementar y surface pieces      184
Elongation kinetics      290
EM density map      27—28 31 364 374
Empirical force field optimization      51
Empirical Force Fields      45
Empirical potential function      360 373—374
ENCAD      50 58 344—345
Energy minimization      2—5 11 339 341 344
Ensemble      30 49 97 101 106 111 171—173 239 271
Ensemble averaging      360 374
Ensemble classifier      171 173
Environmental features      7
EPR      291 295
ESP      52—53
Euclidean distance      77 114 175 185 214
Evolutionary relationship      151 187 166—167 196 319
Ewald method      49
Extended atom force field      58
Family      4 12 21 166 168
Feature vector      162 163 175
FFAS      8
FFT (fast Fourier transform)      25—26

fold      2 5—9 11 23
Fold recognition      6 23 29
Foldlndex      226 238
Force field      2 45
Forward/backward algorithm      268
Fourier transform infrared spectroscopy      286
Fragment      3 8 11 24 129 133—135
Framework      5 71—72 158 328 336 344
FSSP      161 167 176
Function annotation      323
Function prediction      181 195—197
Functional interpretation      359
Fused ball model      182
gaps      97 148 150 155 219 227 229 235 321 323 325—327 344—345
Generalized — Born      50 332 336
Genetic algorithm      11 25—26 267 335 344
Genomes      16 19 29 31 166 226
GenThreader      8
Geometric hashing      26 149 152 155—156 158 160 196
Geometric nature of discrimination      95
Geometric potential function      88 101 105 112 200
Geometry-based procedure      46 181
Global free-energy minimum      9 320
Global optimality      326
GLOBPLOT      226 239
Go models      299
GROMOS      2 46 50 58
Hard-sphere model      182
Helixhunter      28 359 363 373
Hidden Mar kov models (HMM)      8 19 210 213 216 223 234 262 325
HMMSTR      268
Homologous modeling      3—4
Homologous topology      167
Homology detection      6 8—9 29 213 229 324—325
Homology modeling      3—6 9 12—13 18 22—23 25 28 31 230—231 319—322
Homotopy equivalent      184
HP model      10 84 109 298—299
Hydrogen bonds      2 47 208 266 285 296 326 334 342 344
Hydrogen-deuterium exchange      287
Hydrophobic core      23 126 130—131 221 303
Idealized ball model      182
Implicit solvation models      50
Improper angle      46—47 52
Inclusion bodies      281 300
Inclusion-exclusion formula      188 190
Index structure      161—163 174 175
insertion      4—5 192 227 231 289—290 321—323 325—326 330 337—342
Insightll      4 327
Inter-domain, contact      127
Inter-residue contact      274
Interatomic interactions      1—7
Interface, domain      130 138—139 141
Intermediate resolution      27 292 301 359—360
Inverse spherical surface      184
Iterative dynamic programming      153 156 159
Jpred      235—236
K-nearest neighbour (kNN)      210 214 232—233
K-segment clustering      366 368
Kernel voxel      360
Kinetic par titioning      281
Knowledge-based effective potential function      72
Knowledge-based potential      71 73 75—76 85—86 93—94 101—103 108—115
Langevin Dipoles Model      51
Lattice models      10 230 297—299 301
Lee — Richards surface      183
Lennard — Jones (LJ)      46—47 134 302
LevinthaPs Paradox      2 280
Ligand binding      231 291 323 345
Likelihood matrix      264
Limited proteolysis      287—288 291 297
Local conservation      197
Local contacts      257 259 264 265
Local peak filter      366 368
Local structure motifs      268
Locally Delaunay      192—193
Locally enhanced sampling      49
Loop connectivity      359 373
Loop prediction      331—334 338
Loops      5 12 19 134—135 230 259 322—323 327 330—332 336 345 373—374 377
Machine learning      19—20 100 171 210—211 213 215 217 222 232 239 255 257 272—273
Maximum disk inclusion number      360
MD (Molecular- Dynamics simulation)      11 13 56 59 302 336
MD simulation      9 11 20—21 48—52 54—56 291—296 301 303 336
Median of energy value      380
Membrane proteome      21—22
Meta servers      8 16 343—344
Methods, for domain partitioning      125 129
Minimum local thickness      360
Misfolded models      337
Miyazawa — Jernigan contact statistical potential      71
mm      3 66
MMFF      48 58
ModBase      29
Model assessment      336 337
Model building      289 322 325 327—329 333 337—339 343
Model quality      13 335 336 344
Modeling target      3 347—348
Modeller      5 13 24 28—29 327 329 344—345
Molcular surface (MS)      184 287 329
Molecular' dynamics      2 9 20 48 303
Molecular' dynamics simulations      9 11 20—21 48—52 54—56 291—296 301 303 336
Molecular' mechanics      2 45 332
Monte Carlo simulation (MC)      223—224
Morphological analysis      360 366
Morse function      47
Motif      11 20 147 149—150 157—159 166 173 175—176 196—197 221 222 305 320
Multi-dimensional hyperplane      95 100
Multi-domain, chains      142
Multiple sequence alignment      23 207 210 212 228 230 262
Multiple structure alignment      147 149 157 159—161 175—176 325 327
Multiple-domain proteins      22
Native conformation      1 2 72 94 101 106 108 200 331—334 336 341
Native topology      359 360 373—375 377 379—384
Neural network (NN)      19 20 168 171 215—216 222
Non-contiguous, domain      129 132 134 135
Non-local contacts      264 266 269 270 272
Non-order-preserving      150
Non-sequential structure alignment      150
Nonadditivity effect      110
Nucleated growth polymerization      289
Nucleation      270 282 290 303
Nucleation site      270
OPLS      45 50 53—55
OPLS/AA      45 54—56
OPLS/UA      58
Optimal local alignment      324
Optimized linear' potential function      97—98 115
Optimized nonlinear potential function      98 100 106
Or dei' preserving      150
Orthogonal bundle      377
Packing      13 90—91 101 104 112 130
Packing geometry      377
Paiametrization      65
Paii-wise search      325
Par allel tempering      49 181
param      19 181
Parameter optimization      51 56
Partial atomic charges      47 52 55 58
Particle Mesh Ewald      49
Partition function      74 75 106 108 110 111
Partitioning      125—129 133 137—138 142
Pathway models      268
PDB      28 56 142
PDISORDER      226 239
PDP      22 134 139 141
phase diagram      300 303
PHD      212 230 232—233 235—236
Phi, psi angles      52
Photo-affinity labeling      289
Physical potential function      114

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