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| Ïîèñê ïî óêàçàòåëÿì |
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| Bourne P.E., Weissig H. — Structural bioinformatics |
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| Ïðåäìåòíûé óêàçàòåëü |
Semantic elements, macromolecular Crystallographic Information File (mmCIF) data dictionary 169—170
Semiempirical methods, docking and ligand design, scoring functions 456
SEQRES PDB records, ASTRAL compendium secondary data 220—221
SEQRES PDB records, Nucleic Acid Database (NDB) validation 201—202
Sequence alignment, ab initio fold prediction, genome annotation 550
Sequence alignment, ASTRAL compendium sources 220—221
Sequence alignment, CATH domain structure database, homologous structures 253—255
Sequence alignment, CATH domain structure database, relative recruitment 260
Sequence alignment, fold recognition, molecular evolution and sequence similarity 527
Sequence alignment, fold recognition, protein sequence analysis 527—529
Sequence alignment, homology modeling 507—510
Sequence alignment, homology modeling, alignment correction 511—513
Sequence alignment, homology modeling, template identification and alignment 510—511
Sequence alignment, MacroMolecular Database (MMDB) 221—222
Sequence alignment, macromolecular structure, NMR spectroscopy 91
Sequence alignment, Protein Data Bank (PDB), protocol and format 162—164
Sequence alignment, Protein Data Bank (PDB), validation and annotation 186
Sequence alignment, protein structure, amino acid sequence 16—20
Sequence alignment, protein structure, amino acid sequence, amino acid structures 16—17
Sequence alignment, protein structure, amino acid sequence, peptide bonds 17—20
Sequence alignment, protein structure, NMR spectroscopy, sequence-specific assignment 101
Sequence alignment, protein-protein interaction prediction 413
Sequence alignment, protein-protein interaction prediction, computational techniques 418—421
Sequence alignment, protein-protein interaction prediction, hybrid techniques 414—416
Sequence alignment, secondary protein structure, structure assignment 340
Sequence alignment, structural bioinformatics and 4—6
Sequence alignment, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study 597—599
Sequence distribution, secondary structure assignment 351
Sequence Structure Alignment Program (SSAP), CATH domain structure database 252—253
Sequence Structure Alignment Program (SSAP), CATH domain structure database, consensus residue attributes (CORA) 257
Sequence Structure Alignment Program (SSAP), CATH domain structure database, Dictionary of Homologous Superfamilies (DHS) 259—260
Sequence Structure Alignment Program (SSAP), CATH domain structure database, structure-based homologue protocols 255—256
Sequence Structure Alignment Program (SSAP), comparison algorithm optimization 326
Sequence Structure Alignment Program (SSAP), statistical testing 326—327
Sequencespace program, family-dependent conservation 411
Sequential ligand growth, de novo design 449
Server architecture, CATH domain structure database 263—267
Server architecture, one-dimensional secondary structure prediction 566—567
SFCHECK program, Protein Data Bank(PDB) data validation and annotation 186
Shake-and-Bake (SnB) program, high-throughput crystallographic analysis, heavy atom location 77—78
SHARP, high-throughput crystallographic analysis, heavy atom location 78
SHELX software, X-ray crystallography, uncertainty estimation 277
SHELX-D, high-throughput crystallographic analysis, heavy atom location 77—78
Side chains, all-atom contact analysis 310—316
Side chains, amino acid sequence 17
Side chains, error estimation and precision 292
Side chains, homology modeling 508—510 514—516
Side chains, model optimization 516—518
Side chains, protein function identification, pattern comparisons 399
Side chains, tertiary protein structure 28
Signal-to-noise ratio, electron cryomicroscopy, optics and image formation 117—119
Silicon Graphics systems, macromolecular visualization 138—139
Simian Immunodeficiency Virus (SIV), HIV Proteases resource (HIVpr) 225
Simulated tempering, ab initio fold prediction 548—549
Simulation techniques, fold recognition, force fields and threading 533
Simulation techniques, structural bioinformatics 10—11
Single linkage clustering algorithms, CATH domain structure database, sequence-based protocols 253—255
Single nucleotide polymorphisms (SNPs), structural genomics, biomedical applications 604
Single-particle analysis, electron cryomicroscopy, hybrid techniques 123—124
Single-particle analysis, electron cryomicroscopy, three-dimensional reconstruction 122
Site characterization, docking molecule design 445—446
SITE entries, protein function identification 398
Site point connection methods, de novo design 448—449
Site-Match software, protein function identification 398
Six-dimensional search, high-throughput crystallographic analysis, molecular replacement 79
Slide, base pair geometry 48
Small protein classes, SCOP hierarchical classification 241
Solution sets, electron cryomicroscopy/x-ray crystallography procedures 126—127
SOLVE program, high-throughput crystallographic analysis, future applications 83—84
SOLVE program, high-throughput crystallographic analysis, heavy atom location 77—78
Solvent accessibility models, ab initio fold prediction, polypeptide chains 546—547
Solvent accessibility models, docking and ligand design, molecular mechanics scoring functions 459—461
Solvent accessibility models, one-dimensional secondary structure prediction, basic concepts 562—563
Solvent accessibility models, one-dimensional secondary structure prediction, evaluation of 570
Solvent accessible surface area (SASA), docking and ligand design 454 456
Solvent accessible surface area (SASA), docking and ligand design, solvent representation 460—461
Solvent polarization, docking and ligand design, scoring functions 465—466
Solvent-screened interactions, electrostatic interactions 426
Sovation effects, docking and ligand design 444 446
Space mapping, protein folds, structure comparison and alignment 330—332
Space mapping, structural genomics 590
SPARKY program, protein structure, NMR spectroscopy 100—102
SPASM (Spatial Arrangements of Side-chains and Main-chain), protein function identification 399
SPIN-PP database, protein-protein interaction prediction 416
SQUID program, error estimation and precision 296
SSEARCH algorithm, SCOP organization and capabilities 242—244
SSpro algorithm, one-dimensional secondary structure prediction 561—562
Statistical testing, electron cryomicroscopy/x-ray crystallography procedures 126—127
Statistical testing, Protein Data Bank (PDB) data processing 187—188
Statistical testing, structure comparison and alignment 326—327
Status Query interface, Protein Data Bank (PDB), user web access 191—193
Stepwise data management, protein structure, NMR spectroscopy 100—102
Stereo array isotope labeling (SAIL), minimized protein density 105—106
Stereochemical analysis, ASTRAL compendium 220—221
Stereochemical analysis, error estimation and precision, deposited structures 286—289
Stereochemical analysis, nucleic acid chemical structure 44—45
Stereochemical analysis, Protein Data Bank (PDB) data validation 186
Stereochemical Check Score (SCS), ASTRAL compendium 221
STICK protocol, secondary protein structure assignment 353
STRIDE (STRuctural IDEntification) method, automatic assignment comparisons 347—349
STRIDE (STRuctural IDEntification) method, secondary protein structures, empirical hydrogen bond calculation 343
STRIDE (STRuctural IDEntification) method, secondary protein structures, protocols 344—345
Structural bioinformatics, ASTRAL compendium secondary data 220—221
Structural bioinformatics, computing issues 6—7
Structural bioinformatics, data as catalyst for 4—6
Structural bioinformatics, data integration 11
Structural bioinformatics, defined 4
Structural bioinformatics, drug complexes, ADMET modeling 490
Structural bioinformatics, drug complexes, current research 476—477
Structural bioinformatics, drug complexes, future applications 490—491
Structural bioinformatics, drug complexes, historical development 475—476
Structural bioinformatics, drug complexes, lead identification 487—488
Structural bioinformatics, drug complexes, lead optimization 489—490
Structural bioinformatics, drug complexes, pharmaceutical applications 477—479
Structural bioinformatics, drug complexes, target assessment 479—483
Structural bioinformatics, drug complexes, target triage 483—486
Structural bioinformatics, drug complexes, target validation 486—487
Structural bioinformatics, future resources 229—232
Structural bioinformatics, future resources, genomics 231—232
Structural bioinformatics, future resources, interoperability beyond cross-links 231
Structural bioinformatics, future resources, multiple resource integration 229—231
Structural bioinformatics, high-resolution techniques 5—6
Structural bioinformatics, technical challenges 8—11
Structural Classification of Proteins (SCOP), comparison with DALI and CATH 247—248
Structural Classification of Proteins (SCOP), evolutionary mechanisms, structural comparisons 239
Structural Classification of Proteins (SCOP), fold recognition 524
Structural Classification of Proteins (SCOP), fold recognition, algorithm comparison and assessment 540
Structural Classification of Proteins (SCOP), fold recognition, limitations 524—525
Structural Classification of Proteins (SCOP), hierarchical protocols 239—244
Structural Classification of Proteins (SCOP), hierarchical protocols, classes 240—241
Structural Classification of Proteins (SCOP), hierarchical protocols, families 242
Structural Classification of Proteins (SCOP), hierarchical protocols, fold classifications 241
Structural Classification of Proteins (SCOP), hierarchical protocols, superfamilies 242
Structural Classification of Proteins (SCOP), organization and capabilities 242—244
Structural Classification of Proteins (SCOP), PartsList database 227—228
Structural Classification of Proteins (SCOP), principles 10
Structural Classification of Proteins (SCOP), protein fold space mapping 330—332
Structural continuum, CATH domain structure database, fold population statistics 263—264
Structural genomics see also "Genomics"
Structural genomics, ab initio fold prediction 550—551
Structural genomics, database development 231—232
Structural genomics, evolutionary mechanisms 590
Structural genomics, homology modeling 590—591
Structural genomics, homology modeling, databases 591—592
Structural genomics, limitations and drawbacks 606
Structural genomics, NYSGRC case study 597—604
Structural genomics, NYSGRC case study, biomedical implications 604
Structural genomics, NYSGRC case study, evolutionary mechanisms 601
Structural genomics, NYSGRC case study, homology modeling 600—601
Structural genomics, NYSGRC case study, homology modeling, MDD/HSK structures 601
| Structural genomics, NYSGRC case study, progress summary 604—605
Structural genomics, NYSGRC case study, sample preparation and characterization 597—599
Structural genomics, NYSGRC case study, structural overview 599—600
Structural genomics, NYSGRC case study, target selection 597 601—604
Structural genomics, NYSGRC case study, x-ray structure determination 599
Structural genomics, one-dimensional secondary structure prediction 572
Structural genomics, pilot programs 593—597
Structural genomics, Protein Data Bank (PDB) 591
Structural genomics, protein function identification 400—402
Structural genomics, protein sequence information 589—590
Structural genomics, protein structure space 590
Structural genomics, research issues 7
Structural genomics, strategic issues 592
Structural/phylogenetic relationships, CATH domain structure database 252—260
Structure assignment, automatic assignment comparisons 347—349
Structure assignment, empirical calculation 343
Structure assignment, future research issues 351—356
Structure assignment, hydrogen bond models 341—343
Structure assignment, hydrogen bond models, angle-distance assignment 341—342
Structure assignment, hydrogen bond models, Coulomb calculation 342—343
Structure assignment, NMR structures 351
Structure assignment, programs and databases 346—347
Structure assignment, research background 339—341
Structure assignment, secondary structures, assignment techniques 344—346
Structure assignment, secondary structures, assignment techniques, DEFINE algorithm 345
Structure assignment, secondary structures, assignment techniques, DSSP 344
Structure assignment, secondary structures, assignment techniques, DSSPcont 346 353—356
Structure assignment, secondary structures, assignment techniques, P-curve 345—346
Structure assignment, secondary structures, assignment techniques, STRIDE 344—345
Structure assignment, sequence distributions 351
Structure assignment, STICK geometric-based continuous assignment 353
Structure assignment, supersecondary structures 351—353
Structure assignment, three classes conversions 349—351
Structure comparison and alignment, algorithms and optimization 325—326
Structure comparison and alignment, assignment protocols 347—349
Structure comparison and alignment, defined 319—320
Structure comparison and alignment, evaluation of 327—328
Structure comparison and alignment, future applications 332—333
Structure comparison and alignment, homology modeling 507—510
Structure comparison and alignment, homology modeling, alignment correction 511—513
Structure comparison and alignment, homology modeling, template recognition and initial alignment 510—511
Structure comparison and alignment, multiple structure alignment 329—330
Structure comparison and alignment, protein fold space mapping 330—332
Structure comparison and alignment, protein function identification 397
Structure comparison and alignment, protein structures 324—325
Structure comparison and alignment, protocols and methods 322—327
Structure comparison and alignment, sample results 328—329
Structure comparison and alignment, statistical analysis of results 326—327
Structure comparison and alignment, three-dimensional applications 320—321
Structure space exploration, SCOP organization and capabilities 244
Structure-activity relationship homology (SARAH), drug bioinformatics, target triage 486
Structure-activity relationships (SAR), drug bioinformatics 476
Structure-based design, docking molecules and ligands, computer-aided drug design (CADD) 444—445
Structure-based drug design (SBDD), bioinformatics, pharmaceutical models 479
Structure-based drug design (SBDD), structural biology 489—490
Structure-derived potentials, ab initio fold prediction 548
Structure-structure comparisons, ab initio fold prediction, genome annotation 549—550
Structure-structure comparisons, structural genomics 605
STRUDL (STRUctural Domain Limits), domain identification, assignment criteria 378—379
STRUDL (STRUctural Domain Limits), domain identification, second generation assignment algorithms 370—377
Sugar phosphate backbone, nucleic acid structure 49—55
Suiseki system, protein-protein interaction prediction 417
Summary PDB ASTRAL Check Index (SPACI), ASTRAL compendium 221
Superfamilies of proteins, CATH domain structure database, population statistics 264—267
Superfamilies of proteins, CATH domain structure database, superfamily relative recruitment 260
Superfamilies of proteins, fold recognition 523—525
Superfamilies of proteins, SCOP hierarchical classification 239 242
Superfamilies of proteins, structural genomics, target selection 602—604
Supersecondary structures, assignment techniques 351—353
Supramolecular assembly, electrostatic interactions 428
Swiss-Model database, content and protocol 228
Swiss-Model database, homology modeling, backbone generation 513
SwissProt program, MacroMolecular Database (MMDB) 221—222
Symmetry extension dictionary, format and content 175
Syn conformation, sugar phosphate backbone conformation 53—55
Syn conformation, Z-DNA 59
Tabu search, docking and ligand orientation 447—448
Target assessment, drug bioinformatics 479—483
Target assessment, drug bioinformatics, genome druggability 481—483
Target assessment, drug bioinformatics, kinases and ATPases 479—480
Target assessment, drug bioinformatics, proteases 480
Target assessment, drug bioinformatics, rule-of-five quantitative assessment 480—481
Target assessment, fold recognition, algorithm comparison and assessment 539—540
Target assessment, fold recognition, threading errors 537—539
Target assessment, homology modeling 508—510
Target selection, data sources 228—229
Target selection, drug bioinformatics, current research 477
Target selection, one-dimensional secondary structure prediction 572
Target selection, structural bioinformatics 8
Target selection, structural genomics 597
Target selection, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study 601—604
Tautomeric forms, nucleic acid chemical structure 42—45
Taylor expansions, electrostatic interactions, Poisson — Boltzmann equation (PBE), finite difference discretization 433
Template identification and alignment, fold recognition, algorithm comparison and assessment 539—540
Template identification and alignment, fold recognition, threading errors 537—539
Template identification and alignment, homology modeling 508—510
Template identification and alignment, homology modeling, alignment correction 512—513
Template identification and alignment, homology modeling, backbone generation 513
Template identification and alignment, homology modeling, initial alignment 510—511
Template Search and Superposition (TESS), protein function identification 398
Tertiary protein structure, biological fold classification 31—33
Tertiary protein structure, domains and motifs 29
Tertiary protein structure, fold space and evolution 30—31
Tertiary protein structure, fold structure classification 33
Tertiary protein structure, global three-dimensional structure 28—33
Tertiary protein structure, modifications 30
Tertiary protein structure, molecular interaction 29—30
Tertiary protein structure, protein fold 29
Tertiary protein structure, side chains 28
Text strings, macromolecular Crystallographic Information File (mmCIF) 166
TEXTAL program, high-throughput crystallographic analysis, electron density map interpretation 81
Therapeutic index, drug bioinformatics 476
Thermodynamics, docking and ligand design, complex formation 451—454
Thermodynamics, docking and ligand design, research background 442
Thermodynamics, fold recognition, theoretical background 531 533
Thr/Val/Leu tetrahedral branches, all-atom contact analysis 311—316
Threading algorithms, fold recognition, approximations 533—535
Threading algorithms, fold recognition, comparisons 535—536
Threading algorithms, fold recognition, error detection 535 537—539
Threading algorithms, fold recognition, force field calculations 533
Threading algorithms, fold recognition, theoretical background 531 533
Three bond spin-spin coupling, macromolecular structure, NMR spectroscopy 91
Three-dimensional models, all-atom contact analysis 313—316
Three-dimensional models, Cambridge Structural Database (CSD) sources 219
Three-dimensional models, CATH domain structure database 249—252
Three-dimensional models, CATH domain structure database, multiple structure alignments 257
Three-dimensional models, docking and ligand design 442
Three-dimensional models, domain identification, assignment criteria 377—379
Three-dimensional models, domain identification, first generation assignment algorithms 367—370
Three-dimensional models, domain identification, first generation assignment algorithms, physical criteria 369—370
Three-dimensional models, domain identification, first generation assignment algorithms, protein structure classifications 370
Three-dimensional models, domain identification, future research problems 379—380
Three-dimensional models, domain identification, methodological overview 365—367
Three-dimensional models, domain identification, research background 363—365
Three-dimensional models, domain identification, second generation assignment algorithms 370—377
Three-dimensional models, domain identification, second generation assignment algorithms, graph theoretical methods 370—377
Three-dimensional models, domain identification, second generation assignment algorithms, Ising models 377
Three-dimensional models, domain identification, second generation assignment algorithms, TIM barrel structures 377
Three-dimensional models, electron microscopy, crystalline arrays 119—121
Three-dimensional models, electron microscopy, electron tomography 123
Three-dimensional models, electron microscopy, helical assemblies 121
Three-dimensional models, electron microscopy, hybrid techniques 123—124
Three-dimensional models, electron microscopy, imaging protein dynamics 124—125
Three-dimensional models, electron microscopy, research background 115—116
Three-dimensional models, electron microscopy, single-particle analysis 122
Three-dimensional models, homology modeling, alignment correction 511—513
Three-dimensional models, homology modeling, backbone generation 513
Three-dimensional models, homology modeling, design principles 507—510
Three-dimensional models, homology modeling, loop modeling 513—514
Three-dimensional models, homology modeling, optimization 516—518
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