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| Xu Y., Xu D., Liang J. — Computational Methods for Protein Structure Prediction & Modeling. Volume 1 |
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| Ïðåäìåòíûé óêàçàòåëü |
 or  256
 -Lactalbumin 3 321
 -helical 293 295—296 0
-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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