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| Àâòîðèçàöèÿ |
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| Ïîèñê ïî óêàçàòåëÿì |
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| Bourne P.E., Weissig H. — Structural bioinformatics |
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| Ïðåäìåòíûé óêàçàòåëü |
Electron cryomicroscopy, x-ray crystallography and 125—127
Electron density map interpretation, all-atom contact analysis 308—311
Electron density map interpretation, electron cryomicroscopy 116—119
Electron density map interpretation, error estimation and precision, resolution parameters 278—280
Electron density map interpretation, high-throughput crystallographic analysis, macromolecular structure 79—81
Electron density map interpretation, macromolecular visualization 137
Electron optics, electron cryomicroscopy 116—119
Electron tomography, electron cryomicroscopy, three-dimensional reconstruction 123
Electrostatic interactions, functions 425—426
Electrostatic interactions, future applications 435
Electrostatic interactions, high-throughput structures 427—428
Electrostatic interactions, historical evolution 426—427
Electrostatic interactions, Poisson — Boltzmann theory 428—435
Electrostatic interactions, Poisson — Boltzmann theory, energy derivations 430—431
Electrostatic interactions, Poisson — Boltzmann theory, equation elements 428—430
Electrostatic interactions, Poisson — Boltzmann theory, force elements 431—432
Electrostatic interactions, Poisson — Boltzmann theory, multilevel solvers 435
Electrostatic interactions, Poisson — Boltzmann theory, numerical solution 432—435
Electrostatic interactions, Poisson — Boltzmann theory, numerical solution, adaptive finite element discretization 433—435
Electrostatic interactions, Poisson — Boltzmann theory, numerical solution, finite difference discretization 432—433
Electrostatic interactions, research background 426
Electrostatic potential (ESP), docking and ligand design, molecular mechanics scoring functions 458—459
Empirical hydrogen bond calculation, secondary protein structures 343
Empirical scoring functions, docking and ligand design 457
Endo atoms, sugar phosphate backbone conformation 50—55
Energy-based analysis, fold recognition, threading algorithms 534—535
Energy-based analysis, homology modeling, loop regions 514
Enolase superfamily, fold recognition 525
Enrichment factor (EF), docking and ligand design, virtual screening 464
Enthalpy reactions, docking and ligand design 450—454
Entropy reactions, docking and ligand design 450—454
Enzymatic catalysis, evolution of 238—239
Enzyme classification, protein function identification 386—388 393
Enzyme Commission (EC) system, multifunctional protein identification 388
Enzyme Commission (EC) system, protein function identification, analogue structures 395—396
Enzyme Commission (EC) system, protein function identification, enzvme/nonenzyme classification 387—388
Enzyme Commission (EC) system, protein function identification, enzyme function and structural class 393
Enzyme Commission (EC) system, protein function identification, protein folding and 393—394
ERRAT program, error estimation and precision 296
ERRAT program, error estimation and precision, atom-atom contacts 292—294
Error detection and estimation, docking and ligand design 464—465
Error detection and estimation, fold recognition, threading approximations 535 537—539
Error detection and estimation, homology modeling, backbone generation 513
Error detection and estimation, homology modeling, validation procedures 518—519
Error detection and estimation, one-dimensional secondary structure prediction 568—570
Error detection and estimation, Protein Data Bank (PDB) data validation and annotation 186
Error detection and estimation, three-dimensional models 275—296
Error detection and estimation, three-dimensional models, deposited structures 284—296
Error detection and estimation, three-dimensional models, deposited structures, hetero groups 295—296
Error detection and estimation, three-dimensional models, deposited structures, nucleic acids 294—295
Error detection and estimation, three-dimensional models, deposited structures, proteins 289—294
Error detection and estimation, three-dimensional models, deposited structures, serious errors 284—286
Error detection and estimation, three-dimensional models, deposited structures, stereochemical parameters 286—289
Error detection and estimation, three-dimensional models, deposited structures, typical errors 286
Error detection and estimation, three-dimensional models, NMR spectroscopic errors 282—284
Error detection and estimation, three-dimensional models, x-ray crystallographic errors 275—282
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, atomic B-factors 281
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, average positional error 281
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, Bruenger's free R-factor 280—281
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, global parameters 277—281
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, R-factor 280
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, resolution 277—280
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, selection criteria 281—282
Error detection and estimation, three-dimensional models, x-ray crystallographic errors, uncertainty estimation 275—277
Eukaryote structures, one-dimensional secondary structure prediction 573
EVA server, one-dimensional secondary structure prediction, evaluation of programs 568
Evolutionary mechanisms, ab initio fold prediction 548—549
Evolutionary mechanisms, convergent evolution, fold recognition 524
Evolutionary mechanisms, divergent evolution, fold recognition 524
Evolutionary mechanisms, enzymatic catalysis 238—239
Evolutionary mechanisms, fold recognition, molecular evolution 527
Evolutionary mechanisms, homology modeling 507—510
Evolutionary mechanisms, one-dimensional secondary structure prediction, solvent accessibility models 563
Evolutionary mechanisms, one-dimensional secondary structure prediction, theoretical background 559—562
Evolutionary mechanisms, one-dimensional secondary structure prediction, transmembrane helix prediction 565—566
Evolutionary mechanisms, protein structure 237—239
Evolutionary mechanisms, protein structure, fold evolution 238
Evolutionary mechanisms, protein-protein interaction prediction, coevolution 411
Evolutionary mechanisms, protein-protein interaction prediction, conservation of positions 410
Evolutionary mechanisms, protein-protein interaction prediction, family-dependent conservation 411
Evolutionary mechanisms, protein-protein interaction prediction, future applications 421—422
Evolutionary mechanisms, protein-protein interaction prediction, interaction partners 416—421
Evolutionary mechanisms, protein-protein interaction prediction, interaction partners, genomic-based computation 417—418
Evolutionary mechanisms, protein-protein interaction prediction, interaction partners, high-throughput applications 416
Evolutionary mechanisms, protein-protein interaction prediction, interaction partners, protein databases and collections 416—417
Evolutionary mechanisms, protein-protein interaction prediction, interaction partners, sequence-based computation 418—421
Evolutionary mechanisms, protein-protein interaction prediction, interaction regions 411—416
Evolutionary mechanisms, protein-protein interaction prediction, interaction regions, hybrid methods 413—416
Evolutionary mechanisms, protein-protein interaction prediction, interaction regions, sequence-based methods 413
Evolutionary mechanisms, protein-protein interaction prediction, interaction regions, structure-based methods 411—412
Evolutionary mechanisms, protein-protein interaction prediction, research background 409—410
Evolutionary mechanisms, structural genomics, basic concepts 590
Evolutionary mechanisms, structural genomics, yeast mevalonate-5-diphosphale decarboxylase (MDD) case study 601
Evolutionary mechanisms, tertiary protein structure 30—31
Exo atoms, sugar phosphate backbone conformation 50—55
Extensible markup language (XML), format and protocols 176—178
Extensible markup language (XML), Metalloprotein Database and Browser (MDB) 226
Failure detection, docking and ligand design 464—465
Family classifications, CATH domain structure database, superfamily and family population statistics 264—267
Family classifications, fold recognition, multiple alignments 529—531
Family classifications, SCOP hierarchical classification 239 242
Family-dependent conservation, protein-protein interaction prediction 411
Fast Fourier transform (FFT), high-throughput crystallographic analysis, electron density map interpretation 80
Fast Fourier transform (FFT), high-throughput crystallographic analysis, refinement techniques 82
Fast Fourier transform (FFT), ligand orientation 447—448
FASTA algorithm, fold recognition, protein sequence analysis 528—529
FASTA algorithm, homology modeling, template identification and alignment 510—511
FASTA algorithm, SCOP organization and capabilities 242—244
Ferredoxinlike fold, protein function identification 393—394
Fibrous proteins, biochemical classification 33
Fibrous proteins, structural bioinformatics 7
Fibrous proteins, tertiary protein structure 30
Field emission gun (FEG) electron source, electron cryomicroscopy, optical resolution 118—119
File transfer protocol (ftp), Protein DataBank (PDB), access protocols 194
File transfer protocol (ftp), Protein DataBank (PDB), architecture 190—191
Finite difference discretization, electrostatic interactions, Poisson — Boltzmann equation (PBE) 432—433
First generation assignment algorithms, domain identification 367—370
First generation assignment algorithms, domain identification, physical criteria 369—370
First generation assignment algorithms, domain identification, protein structure classifications 370
First principles methods, docking and ligand design, scoring functions 456
Flexible ligands, docking procedures 448
FlexX, docking and ligand design, success/failure testing 463
FlexX, ligand site characterization 445—446
Flipkin script, all-atom contact analysis 313—316
Floppy proteins, one-dimensional secondary structure prediction 573
Fold recognition see also "Protein folding"
Fold recognition, algorithm comparison and assessment 539—540
Fold recognition, Critical Assessment for Structure Prediction (CASP) 503
Fold recognition, Critical Assessment for Structure Prediction (CASP), novel recognition 503—504
Fold recognition, error detection in threading 535 537—539
Fold recognition, homology modeling 510
Fold recognition, homology modeling, sequence-only distant homology algorithms 531—532
Fold recognition, homology modeling, theoretical background 527
Fold recognition, modeling applications 523—525
Fold recognition, molecular evolution 527
Fold recognition, protein families and multiple alignments 529—531
Fold recognition, protein sequence analysis 527—529
Fold recognition, sequence similarity 527
Fold recognition, sequence-only algorithms 531—532
Fold recognition, simulation and threading force fields 533
Fold recognition, theoretical background 526
Fold recognition, threading approximations 533—535
Fold recognition, threading approximations, algorithms 536
Fold space, structural genomics 590
Fold space, structure comparison and alignment 330—332
Fold space, tertiary protein structure 30—31
Force field evaluation see also "Potentials of mean force (PMF)"
Force field evaluation, electrostatic interactions, Poisson — Boltzmann equation (PBE) 431—432
Force field evaluation, fold recognition, threading algorithms 533
Force field evaluation, homology model optimization 516—518
| Force field evaluation, homology model optimization, validation procedures 518—519
Fourier transform (FT), electron cryomicroscopy, optics and image formation 116—119
Fourier transform (FT), electron cryomicroscopy, three-dimensional crystalline arrays 119—121
Fourier transform (FT), structural bioinformatics, crystallographic data 8
Fragment placement, ab initio fold prediction, polypeptide chains 546—547
Fragment placement, de novo design 448
Free energy perturbation (FEP), docking and ligand design, scoring techniques 456—457
Free energy, docking and ligand design, binding sites 463—464
Free energy, docking and ligand design, complex formation principles 450—454
Free energy, docking and ligand design, energy interactions 450—451
Free energy, docking and ligand design, molecular mechanics/continuous solvent models 466
Free energy, docking and ligand design, rank ordering 463
Free energy, docking and ligand design, research background 442
Free energy, drug bioinformatics, target druggability 481
Free energy, electrostatic interactions, Poisson — Boltzmann equation (PBE) 430—431
FRODO software, macromolecular visualization 136 138
FSSP database, continuous Dictionary of Secondary Structure of Proteins (DSSPcont) 353—356
FSSP database, domain identification, assignment criteria 377—379
FSSP database, domain identification, fold recognition, limitations 524—525
FSSP database, domain identification, second generation assignment algorithms 370—377
FTDock, ligand orientation 447—448
Function derivation, protein structure, ab initio prediction 396—397
Function derivation, protein structure, analogues 395—396
Function derivation, protein structure, assignment protocols 396—402
Function derivation, protein structure, database classification 388—390
Function derivation, protein structure, definitions 386
Function derivation, protein structure, enzyme function 393
Function derivation, protein structure, enzyme/nonenzyme classification 386—388
Function derivation, protein structure, Fuzzy Functional Forms (FFF) algorithm 398—399
Function derivation, protein structure, gene ontologies 388 391
Function derivation, protein structure, genomic applications 400—402
Function derivation, protein structure, genomic applications, IMPase 402
Function derivation, protein structure, genomic applications, Mj0577-putative Atp molecular switch 400—401
Function derivation, protein structure, genomic applications, YcaC-bacterial hydrolase 401—402
Function derivation, protein structure, homologous families 393 395
Function derivation, protein structure, molecular recognition 399
Function derivation, protein structure, multifunctional proteins 388
Function derivation, protein structure, protein fold and 393—394
Function derivation, protein structure, protein-ligand complexes 391—392
Function derivation, protein structure, research background 385—386
Function derivation, protein structure, RIGOR tool 399
Function derivation, protein structure, side chain patterns 399
Function derivation, protein structure, SITE and Site-Match 398
Function derivation, protein structure, SPASM tool 399
Function derivation, protein structure, structural comparisons 397
Function derivation, protein structure, structural motifs 397—399
Function derivation, protein structure, TESS algorithm 398
Function derivation, protein structure, three-dimensional structures 391—392
Fuzzy Functional Forms (FFFs), protein function identification 398—399
Galerkin discretization, electrostatic interactions, Poisson — Boltzmann equation (PBE) 434—435
Gaps, fold recognition, protein sequence analysis 528—529
GARANT, protein structure, NMR spectroscopy 100—102
Gauche values, sugar phosphate backbone conformation 55
GenBank program, CATH domain structure database 247—248
GenBank program, MacroMolecular Database (MMDB) 221—222
Gene fusion, protein-protein interaction prediction 418
Gene neighboring conservation, protein-protein interaction prediction 417—418
Gene ontology, protein function identification 388 391
GENE3D resource, CATH domain structure database 260—261
GeneFold algorithm, fold recognition 540
Generalized Born model, docking and ligand design, solvent representation 460—461
Genetic algorithms, ab initio fold prediction 548—549
Genome sequencing see also "Structural genomics"
Genome sequencing, ab initio fold prediction 549—550
Genome sequencing, MacroMolecular Database (MMDB) 221—222
Genome sequencing, one-dimensional secondary structure prediction 571—572
Genome sequencing, structural bioinformatics 5
Genomics see also "Structural genomics"
Genomics, drug bioinformatics, druggability studies 481—483
Genomics, protein-protein interaction prediction computational methods 417—418
Genomics, research background 409—410
Genomics, secondary protein structure, structure assignment 339—340
Geometric analysis, ab initio fold prediction, genome annotation 549—550
Geometric analysis, docking and ligand design, reassembly complexes 462—463
Geometric analysis, PDB quality information 298
GHMP kinases, homology modeling, yeast mevalonale-5-diphosphate decarboxylase (MDD) ease study 600—601
GHMP kinases, structural genomics, biomedical applications 604
GHMP kinases, structural genomics, target selection 602—604
Global alignment method, CATH domain structure database, sequence-based protocols 253—255
Globular proteins, biochemical classification 31—32
Glycine, peptide bond structure 19—20
Glycine, side chain sequence 17
Glycosidic bond, nucleic acid chemical structure 43—45
Glycosidic bond, sugar phosphate backbone conformation 50—55
Graph theoretical techniques, domain identification, second generation assignment algorithms 370—377
Graphical Method for Identifying Folds (GRATH), CATH domain structure database, domain boundary identification 258
Graphical Method for Identifying Folds (GRATH), CATH domain structure database, homologous structural analysis 256—257
Greek-key motifs, secondary structure assignment 351—353
GRID software, drug bioinformatics, chemical lead identification 488
Groove interactions, DNA duplexes 56—59
Groove interactions, DNA-drug interactions 59—60
Groove interactions, Nucleic Acid Database (NDB) data 208—210
Hairpin loops, secondary protein structure 24—28
Hammerhead ribozymes 61 64
HAMMERHEAD software, ligand orientation 447—448
Handedness,  -helices 22—24
Heavy atoms, all-atom contacts, Met conformations 312—316
Heavy atoms, all-atom contacts, structure validation 305—307
Heavy atoms, high-throughput crystallographic analysis, macromolecular structures 77—78
Helical twist, base pair geometry 48
Helices, DNA structure 41—42
Helices, duplex RNA 60—62
Helices, electron cryomicroscopy, hybrid techniques 123—124
Helices, electron cryomicroscopy, pattern recognition 128
Helices, electron cryomicroscopy, three-dimensional reconstruction 121
Helices, Nucleic Acid Database (NDB) data 207—210
Helices, one-dimensional secondary structure prediction, evolution of techniques 570—571
Helices, one-dimensional secondary structure prediction, transmembrane helix prediction 563—566
Helices, rare structures, secondary protein structure 24
Helices, ribosomal RNA 64—67 see
Hershey — Chase experiments, DNA structure 41
Hetero compounds, error estimation and precision 295—296
HETZE program, error estimation and precision, hetero compounds 295—296
Hidden Markov models (HMMs), fold recognition, divergent evolution 524
Hidden Markov models (HMMs), fold recognition, protein families, multiple alignments 530—532
Hidden Markov models (HMMs), one-dimensional secondary structure prediction 561—562
Hidden Markov models (HMMs), one-dimensional secondary structure prediction, evaluation of techniques 571
Hidden Markov models (HMMs), one-dimensional secondary structure prediction, transmembrane helix prediction 566
Hidden Markov models (HMMs), structural comparison and alignment 328—329
High scoring fragments (HSF), fold recognition, protein sequence analysis 528—529
High-resolution techniques, biological structures 5—6
High-throughput crystallographic analysis, drug bioinformatics 477
High-throughput crystallographic analysis, drug bioinformatics, pharmaceutical models 478—479
High-throughput crystallographic analysis, electrostatic interactions 427—428
High-throughput crystallographic analysis, macromolecular structure, automation issues 82—83
High-throughput crystallographic analysis, macromolecular structure, data analysis techniques 76—77
High-throughput crystallographic analysis, macromolecular structure, density modification 78
High-throughput crystallographic analysis, macromolecular structure, disorder 83
High-throughput crystallographic analysis, macromolecular structure, heavy atom location and computation 77—78
High-throughput crystallographic analysis, macromolecular structure, map interpretation 79—81
High-throughput crystallographic analysis, macromolecular structure, molecular replacement 78—79
High-throughput crystallographic analysis, macromolecular structure, noncrystallographic symmetry 82—83
High-throughput crystallographic analysis, macromolecular structure, principles 76
High-throughput crystallographic analysis, macromolecular structure, refinement methods 81—82
High-throughput crystallographic analysis, macromolecular structure, research background 75
High-throughput crystallographic analysis, macromolecular structure, validation 82
High-throughput crystallographic analysis, protein-protein interaction partners 416
High-throughput crystallographic analysis, structural genomics 592
HIV Proteases resource (HIVpr), data content 225
Homology modeling, alignment correction 511—513
Homology modeling, backbone generation 513
Homology modeling, CATH domain structure database, Sequence Structure Alignment Program (SSAP) protocols 255—256
Homology modeling, CATH domain structure database, sequence-based protocols 253—255
Homology modeling, CATH domain structure database, superfamily dictionaries 259—260
Homology modeling, design principles 507—510
Homology modeling, fold recognition, comparisons 523—525
Homology modeling, fold recognition, molecular evolution and sequence similarity 527
Homology modeling, fold recognition, protein families and multiple alignments 529—531
Homology modeling, fold recognition, protein sequence analysis 528—529
Homology modeling, loop modeling 513—514
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