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| Ïîèñê ïî óêàçàòåëÿì |
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| Bourne P.E., Weissig H. — Structural bioinformatics |
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| Ïðåäìåòíûé óêàçàòåëü |
Computational techniques, protein-protein interaction prediction, genomics-based compulation 417—418
Computational techniques, protein-protein interaction prediction, sequence-based information 418—421
Computer-aided drug design (CADD), docking molecules 444—450
Computer-aided drug design (CADD), docking molecules, analog-based design 444—445
Computer-aided drug design (CADD), docking molecules, structure-based design 445—449
Computer-aided drug design (CADD), docking molecules, virtual library design 449—450
Computer-aided drug design (CADD), drug bioinformatics 477
Computer-aided molecular design, methods and tools 443
Computer-aided target selection (CATS), drug bioinformatics, target triage 484—486
Conformational analysis, ab initio fold prediction, polypeptide chains 546—547
Conformational analysis, docking molecules and ligands, computer-aided drug design (CADD) 444—445
Connecting/disconnecting technique, de novo design, sequential ligand grow 449
Consensus residue attributes (CORA), CATH domain structure database, multiple structure alignments 257
Conservation of positions see also "Family-dependent conservation"
Conservation of positions, gene neighboring conservation 417—418
Conservation of positions, protein-protein interaction prediction 410
Continuous Dictionary of Secondary Structure of Proteins (DSSPcont), secondary protein structure assignment 353—356
Continuum water models, docking and ligand design, solvent representation 460—461
Contrast-transfer function (CTF), electron cryomicroscopy 116—119
Convergent evolution, fold recognition 524
Cooperativity, quaternary protein structure 35
Core relational database, Protein Data Bank (PDB) 190—191
Correct amino acid partners-correct, interactions approximation, fold recognition, threading errors 537—539
Correct amino acid partners-wrong interactions approximation, fold recognition, threading errors 538—539
Correct partners-correct interactions (CC), approximation, fold recognition, threading errors 535 537—539
Correct partners-wrong interactions (CW), approximation, fold recognition, threading errors 537—539
Correlated mutations, protein-protein interaction prediction 411
Correlated mutations, protein-protein interaction prediction, hybrid prediction techniques 414—416
Correlated mutations, protein-protein interaction prediction, sequence-based analysis 413 418—419
Correlated spectroscopy (COSY), quality assurance 274
Coulomb hydrogen bond calculation, secondary protein structures 342—343
Coulombic interactions, docking and ligand design, complex formation 450—454
Coulombic interactions, docking and ligand design, solvent accessible surface area (SASA) 454 456
Covalent bond distances and angles, Protein Data Bank (PDB) data acquisition 186
Covalent interactions, DNA-drug interactions 59—60
Covalent interactions, tertiary protein structure 30
Critical Assessment for Structure Prediction (CASP), ab initio fold prediction, polypeptide chains 546—547
Critical Assessment for Structure Prediction (CASP), Critical Assessment of Fully Automated Structure Prediction (CAFASP) evolution 504
Critical Assessment for Structure Prediction (CASP), fold recognition, algorithm comparison and assessment 539—540
Critical Assessment for Structure Prediction (CASP), fold recognition, protein families, multiple alignments 530—531
Critical Assessment for Structure Prediction (CASP), homology modeling 510
Critical Assessment for Structure Prediction (CASP), one-dimensional secondary structure prediction, evaluation of programs 567—568
Critical Assessment for Structure Prediction (CASP), one-dimensional secondary structure prediction, system comparisons 561—562
Critical Assessment for Structure Prediction (CASP), principles 10
Critical Assessment for Structure Prediction (CASP), target and prediction data 228—229
Critical Assessment for Structure Prediction (CASP), three-dimensional modeling, comparative modeling 502—503
Critical Assessment for Structure Prediction (CASP), three-dimensional modeling, fold recognition 503
Critical Assessment for Structure Prediction (CASP), three-dimensional modeling, novel fold recognition 503—504
Critical Assessment for Structure Prediction (CASP), three-dimensional modeling, research background 499—501
Critical Assessment for Structure Prediction (CASP), three-dimensional modeling, summary of progress 501—502
Critical Assessment of Fully Automated Structure Prediction (CAFASP), evolution of 504
Critical Assessment of Fully Automated Structure Prediction (CAFASP), fold recognition, algorithm comparison and assessment 539—540
Critical Assessment of Fully Automated Structure Prediction (CAFASP), one-dimensional secondary structure prediction, evaluation of programs 568
Critical Assessment of Fully Automated Structure Prediction (CAFASP), three-dimensional modeling, comparative modeling 502—503
Critical Assessment of Fully Automated Structure Prediction (CAFASP), three-dimensional modeling, fold recognition 503
Critical Assessment of Fully Automated Structure Prediction (CAFASP), three-dimensional modeling, novel fold recognition 503—504
Critical Assessment of Fully Automated Structure Prediction (CAFASP), three-dimensional modeling, research background 499—501
Critical Assessment of Fully Automated Structure Prediction (CAFASP), three-dimensional modeling, summary of progress 501—502
Critical Assessment of Predicted Interactions (CAPRI) system, docking and ligand design 467
Critical Assessment of Predicted Interactions (CAPRI) system, protein docking studies 412
Cross validation, high-throughput, crystallographic analysis, macromolecular structure 81—82
Cross-links, database interoperability 231
Cryo-EM dictionary, format and content 175
Crystal packing, A-DNA structure 58—59
Crystalline arrays, electron cryomicroscopy, three-dimensional reconstruction 119—121
Crystallization analysis see also "X-ray crystallography"
Crystallization analysis, data sources, Biological Macromolecule Crystallization Database (BMCD) 218—219
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF) 164—175
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), atomic positions 173—175
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), dictionary content 170—175
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), molecular entitites 171
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), polymer and non-polymer entities 172—173
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), semantic elements 169—170
Crystallization analysis, macromolecular Crystallographic Information File (mmCIF), syntax structure 165—169
Crystallization analysis, macromolecular structure, vs. nuclear magnetic resonance (NMR) spectroscopy 90
Crystallization analysis, nucleic acid chemical structure 42—45
Crystallization analysis, Nucleic Acid Database (NDB) data 208—210
Crystallization analysis, structural bioinformatics 8
Crystallization analysis, structural bioinformatics, simulation techniques 10—11
Crystallographic Information File (CIF), Cambridge Structural Database (CSD) 219—220
Cup change, base pair geometry 46—47
Cyclic model refinement, electron cryomicroscopy, single-particle analysis 122
Cyclooxygenase (COX), drug bioinformatics 476
Cytochrome P450, ADMET modeling 490
Cytoskeleton structures, three-dimensional reconstruction, crystalline arrays 121
Cytoskeleton structures, three-dimensional reconstruction, helical assemblies 121
D-amino acids, protein structure, error, estimation and precision 290—292
DACA method, error estimation and precision, atom-atom contacts 294
DALI domain structure database, comparison algorithm optimization 325
DALI domain structure database, comparison with SCOP and CATH 247—248
DALI domain structure database, fold recognition algorithms 540
DALI domain structure database, historical development 249
DALI domain structure database, protein structure comparison and alignment 324
DALI domain structure database, statistical testing 326
DAS program, one-dimensional secondary, structure prediction, transmembrane helix prediction 566
Data blocks, macromolecular Crystallographic Information File (mmCIF) 167—168
Data management, high-throughput crystallographic analysis, macromolecular structures 76—77
Data management, macromolecular structure, data flow diagram 215 218
Data management, macromolecular structure, macromolecular Crystallographic Information File (mmCIF) 164—175
Data management, macromolecular structure, NMR spectroscopy 91—94
Data management, Protein Data Bank (PDB) 182—189
Data management, Protein Data Bank (PDB), content characteristics 184
Data management, Protein Data Bank (PDB), deposition sites 187
Data management, Protein Data Bank (PDB), format and protocols 162—164
Data management, Protein Data Bank (PDB), statistics 187
Data management, Protein Data Bank (PDB), uniformity protocols 187—189
Data management, Protein Data Bank (PDB), validation and annotation 184—186
Data management, protein structures, NMR spectroscopy 99—102
Data management, structural bioinformatics 4—6
Data management, structural bioinformatics, crystallographic data 8
Data management, structural bioinformatics, integration techniques 11
Data management, structural bioinformatics, molecular structural data storage 9
Database architecture, docking and ligand design 466—467
Database architecture, Nucleic Acid Database (NDB) 202—204
Database architecture, one-dimensional secondary structure prediction 572—573
Database architecture, Protein Data Bank (PDB) 190—191
Database architecture, protein function identification 388—390
Database architecture, secondary protein structure, assignment protocols 346—347
Database architecture, structural genomics, homology modeling 591—592
Daunomvein, B-DNA structure 56—57
De novo design, connection methods 448—449
De novo design, docking molecules and ligands 445
De novo design, fragment placement 448
De novo design, sequential grow 449
Debye — Huckel parameter, electrostatic interactions, Poisson — Boltzmann equation (PBE) 430
DEFINE algorithm, automatic assignment comparisons 347—349
DEFINE algorithm, secondary protein structure assignment 345
Degrees of freedom, docking and ligand design, combinatorial calculation 461
Density correlation measurements, electron cryomicroscopy/x-ray crystallography procedures 126—127
Density modification, high-throughput crystallographic analysis, macromolecular structure 78
Deposited structures, error estimation and precision 284—296
Deposited structures, hetero groups 295—296
Deposited structures, nucleic acids 294—295
Deposited structures, proteins 289—294
Deposited structures, serious errors 284—286
Deposited structures, stereochemical parameters 286—289
Deposited structures, typical errors 286
Deposition procedures, Protein Data Bank (PDB) data deposition 187
Deposition procedures, protein structure, NMR spectroscopy 102
DETECTIVE algorithm, domain identification, assignment criteria 378—379
DETECTIVE algorithm, domain identification, CATH domain structure database 258
DETECTIVE algorithm, domain identification, first generation assignment 369—370
DETECTIVE algorithm, domain identification, second generation assignment algorithm 374—377
Dickerson dodecamer, DNA duplexes 56—57
Dictionary Definition Language (DDL), macromolecular Crystallographic Information File (mmCIF) 165—170
Dictionary of Homologous Superfamilies (DHS), CATH domain structure database 259—260
Dictionary of Secondary Structure of Proteins (DSSP), automatic assignment comparisons 347—349
Dictionary of Secondary Structure of Proteins (DSSP), conversion to three classes 349—351
Dictionary of Secondary Structure of Proteins (DSSP), data sources 222
Dictionary of Secondary Structure of Proteins (DSSP), one-dimensional secondary structure prediction, solvent accessibility models 562—563
| Dictionary of Secondary Structure of Proteins (DSSP), structural assignment, Coulomb hydrogen bond calculation 342—343
Dictionary of Secondary Structure of Proteins (DSSP), structural assignment, protocols 344
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF) 164—175
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), atomic positions 173—175
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), dictionary content 170—175
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), molecular entitites 171
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), polymer and non-polymer entities 172—173
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), semantic elements 169—170
Dictionary-based data management, macromolecular Crystallographic Information File (mmCIF), syntax structure 165—169
Dielectric constant, docking and ligand design, solvent representation 460—461
Difference mapping, electron cryomicroscopy/x-ray crystallography procedures 127
Diffusion equation, electrostatic interactions 427
Dihydrofolate reductase (DHFR), docking and ligand design, experimental model 454—455
DIP database, protein-protein interaction prediction 417
Dipolar coupling, macromolecular structure, NMR spectroscopy 91
Dipolar coupling, NMR structures, error estimates 283—284
Dirac delta functions, electrostatic interactions, Poisson equation 428—430
Discretization techniques, electrostatic interactions, Poisson — Boltzmann equation (PBE), adaptive finite clement discretization 433—435
Discretization techniques, electrostatic interactions, Poisson — Boltzmann equation (PBE), finite difference discretization 432—433
Disorder, high-throughput crystallographic analysis, macromolecular structures 83
Distance mapping, domain identification, first generation assignment algorithms 369—370
Distance matrices, protein structure comparison and alignment DALI database 324
Distant homology, ab initio fold prediction, genome annotation 549—550
Distant homology, fold recognition 525
Distant homology, fold recognition, protein families, multiple alignments 530—532
Distant waters, Protein Data Bank (PDB) data validation and annotation 186
Distribution protocols, Divergent evolution, fold recognition 524
Distribution protocols, Nucleic Acid Database (NDB) 204—206
DNA, electrostatic interactions 426
DNA, Nucleic Acid Database (NDB) information 200—201
DNA, sequencing 3—4
DNA, structural characteristics 41—42
DNA, structural characteristics, base pair geometry 45—49
DNA, structural characteristics, duplexes 55—59
DNA, structural characteristics, quadruplexes 60
DNA, structural characteristics, sugar phosphate backbone 49—55
DnaK chaperon, correlation mutation 413
DnaK chaperon, correlation mutation, DNA quadruplexes, structural characteristics 57 60
DOCK software, docking and ligand design, reassembly complexes 462—463
DOCK software, docking and ligand design, scoring techniques 456
DOCK software, docking and ligand design, success/failure testing 463
DOCK software, docking molecule site characterization 445—446
Docking molecules, design principles, ADME properties 468
Docking molecules, design principles, combinatorial calculation 461
Docking molecules, design principles, complex formation flow chart 450—454
Docking molecules, design principles, computer-aided drug design (CADD) 444—450
Docking molecules, design principles, computer-aided drug design (CADD), analog-based design 444—445
Docking molecules, design principles, computer-aided drug design (CADD), structure-based design 445—449
Docking molecules, design principles, computer-aided drug design (CADD), virtual library design 449—450
Docking molecules, design principles, database organization 466—467
Docking molecules, design principles, de novo design cycles 443
Docking molecules, design principles, experimental conditions 454—455
Docking molecules, design principles, free energies and energy binding 450
Docking molecules, design principles, future scoring techniques 465—466
Docking molecules, design principles, landscape models 467
Docking molecules, design principles, macromolecular docking 467
Docking molecules, design principles, molecular mechanics scoring, parametrization 457—461
Docking molecules, design principles, molecular mechanics scoring, parametrization, charge representation 457—459
Docking molecules, design principles, molecular mechanics scoring, parametrization, solvent representation 459—461
Docking molecules, design principles, molecular mechanics scoring, parametrization, van der Waals radii 459
Docking molecules, design principles, pharmacogenetics 468
Docking molecules, design principles, research background 441—443
Docking molecules, design principles, scoring functions 456—457
Docking molecules, design principles, scoring functions, empirical methods 457
Docking molecules, design principles, scoring functions, first principles methods 456
Docking molecules, design principles, scoring functions, knowledge-based potentials 457
Docking molecules, design principles, scoring functions, semiempirical methods 456
Docking molecules, design principles, solvation/hydration effects 454 456
Docking molecules, design principles, testing procedures 462—465
Docking molecules, design principles, testing procedures, complex reassembly 462—464
Docking molecules, design principles, testing procedures, failure testing 464—465
Docking molecules, design principles, testing procedures, virtual screening 464
Docking molecules, electron cryomicroscopy/x-ray crystallography procedures 126—127
Docking molecules, macromolecular docking 467
Docking molecules, protein interaction region predictions 411—412
Docking molecules, protein interaction region predictions, future research 421—422
Docking molecules, protein interaction region predictions, hybrid prediction techniques 413—416
Document Type Definition (DTD), format and protocols 176—178
Domain structures, CATH domain structure database, boundary identification 258
Domain structures, CATH domain structure database, CENE3D resource 260—261
Domain structures, CATH domain structure database, comparison with SCOP and DALI 247—248
Domain structures, CATH domain structure database, historical development 248—252
Domain structures, CATH domain structure database, homologous structures, sequence-based protocols 253—255
Domain structures, CATH domain structure database, homologous structures, structure-based methods 255—257
Domain structures, CATH domain structure database, homologous structures, superfamily dictionaries 259—260
Domain structures, CATH domain structure database, homologous structures, superfamily sequence relatives 260
Domain structures, CATH domain structure database, multiple structure alignments 3D templates 257
Domain structures, CATH domain structure database, population statistics, folds in architectures 263—264
Domain structures, CATH domain structure database, population statistics, superfamily/family folds 264—267
Domain structures, CATH domain structure database, server applications 263—267
Domain structures, CATH domain structure database, structural/phylogenetic identification 249—260
Domain structures, CATH domain structure database, web site and server protocols 261—263
Domain structures, electrostatic interactions 427—428
Domain structures, identification techniques, assignment criteria 377—379
Domain structures, identification techniques, first generation assignment algorithms 367—370
Domain structures, identification techniques, first generation assignment algorithms, physical criteria 369—370
Domain structures, identification techniques, first generation assignment algorithms, protein structure classifications 370
Domain structures, identification techniques, future research problems 379—380
Domain structures, identification techniques, methodological overview 365—367
Domain structures, identification techniques, research background 363—365
Domain structures, identification techniques, second generation assignment algorithms 370—377
Domain structures, identification techniques, second generation assignment algorithms, graph theoretical methods 370—377
Domain structures, identification techniques, second generation assignment algorithms, Ising models 377
Domain structures, identification techniques, second generation assignment algorithms, TIM barrel structures 377
Domain structures, SCOP hierarchical classification 240—241
Domain structures, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study 599—600
Domain structures, tertiary protein structure 29
Domain-domain interfaces, domain identification 379—380
DomainFinder algorithm, CATH domain structure database, GENE3D resource 261
DomainParser, domain identification, second generation assignment algorithm 377
DOMAK system, domain identification, assignment criteria 378—379
DOMAK system, domain identification, protein structure classification 370
DOMAK system, domain identification, second generation assignment algorithm 374—377
Double dynamic programming, Sequence Structure Alignment Program (SSAP) 326
Double helix, base pair geometry 45—49
Double helix, DNA structure 41—42
Double helix, Nucleic Acid Database (NDB) data 207—210
Drug complexes, computer-aided drug design (CADD) 444—450
Drug complexes, computer-aided drug design (CADD), analog-based design 444—445
Drug complexes, computer-aided drug design (CADD), structure-based design 445—449
Drug complexes, computer-aided drug design (CADD), virtual library design 449—450
Drug complexes, nucleic acid structure and 59—60
Drug complexes, pharmacogenetics 468
Drug complexes, structural bioinformatics, ADMET modeling 490
Drug complexes, structural bioinformatics, current research 476—477
Drug complexes, structural bioinformatics, future applications 490—491
Drug complexes, structural bioinformatics, historical development 475—476
Drug complexes, structural bioinformatics, lead identification 487—488
Drug complexes, structural bioinformatics, lead optimization 489—490
Drug complexes, structural bioinformatics, pharmaceutical applications 477—479
Drug complexes, structural bioinformatics, target assessment 479—483
Drug complexes, structural bioinformatics, target triage 483—486
Drug complexes, structural bioinformatics, target validation 486—487
Duplex DNA, structural properties 55—59
Duplex RNA, structural properties 60—62
DYANA program, protein structure, NMR spectroscopy 100—102
DYANA program, protein structure, NOE assignment and structure calculation 102
DYANA program, protein structure, validation 103
Electron cryomicroscopy, development 115—116
Electron cryomicroscopy, electron optics and image formation 116—119
Electron cryomicroscopy, future research 128—129
Electron cryomicroscopy, pattern recognition 127—128
Electron cryomicroscopy, research background 115—116
Electron cryomicroscopy, three-dimensional reconstruction 119—125
Electron cryomicroscopy, three-dimensional reconstruction, crystalline arrays 119—121
Electron cryomicroscopy, three-dimensional reconstruction, electron tomography 123
Electron cryomicroscopy, three-dimensional reconstruction, helical assemblies 121
Electron cryomicroscopy, three-dimensional reconstruction, hybrid techniques 122—123
Electron cryomicroscopy, three-dimensional reconstruction, protein dynamics imaging 123—124
Electron cryomicroscopy, three-dimensional reconstruction, single-particle analysis 122
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