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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 |
Homology modeling, optimization 516—518
Homology modeling, protein function identification 393 395
Homology modeling, side-chain modeling 514—516
Homology modeling, structural genomics, basic concepts 590—591
Homology modeling, structural genomics, databases 591—592
Homology modeling, structural genomics, MDD/HSK structures 601
Homology modeling, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study 600—601
Homology modeling, template recognition and initial alignment 510—511
Homology modeling, validation procedures 518—519
Homoserine kinases (HSK), structural genomics, homology modeling 600—601
Homoserine kinases (HSK), structural genomics, target selection 602—604
HOMSTRAD data base, multiple structure alignments 330
HSQC techniques, macromolecular structure, NMR screening 94—96
Human Genome Project, structural genomics 592
Human immunodeficiency virus, HIV Proteases resource (HIVpr) 225
Hybrid microscopic techniques, electron cryomicroscopy 123—124
Hybrid prediction techniques, protein-protein interactions 413—416
Hydration, B-DNA structure 57—58
Hydration, docking and ligand design 444 446
Hydration, Nucleic Acid Database (NDB) data 207—210
Hydration, Z-DNA 59
Hydrogen atoms, all-atom contacts, structure validation 304—317
Hydrogen bond models,  -helices 22—23
Hydrogen bond models, base pair geometry 45—49
Hydrogen bond models, Dictionary of Secondary Structure of Proteins (DSSP) techniques 344
Hydrogen bond models, secondary protein structures, assignment 341—343
Hydrogen bond models, secondary protein structures, assignment, angle-distance assignment 341—342
Hydrogen bond models, secondary protein structures, assignment, Coulomb calculation 342—343
Hydrogen bond models, secondary protein structures, assignment, future research 352—353
Hydrophic amino acids, side chain sequence 17
Hydrophobic effect, one-dimensional secondary structure prediction, solvent accessibility models 563
Hydrophobic effect, one-dimensional secondary structure prediction, transmembrane helix prediction 566
Hydrophobic effect, tertiary protein structure 29—30
I-sites, secondary structure assignment 351—353
i2h prediction method, protein-protein interaction prediction, sequence-based computation 419
Image formation, electron cryomicroscopy, optical resolution 116—119
Image formation, electron cryomicroscopy, protein dynamics 124—125
Image formation, electron cryomicroscopy, three-dimensional reconstruction 119—125
ImgCIF dictionary, format and content 175
IMPALA algorithm, CATH domain structure database, sequence-based homologue protocols 253—255
IMPase structure, protein function identification 402
Inclination, base pair geometry 47
Inelastic scattering, electron cryomicroscopy 117—119
Insertions, fold recognition, protein sequence analysis 528—529
Inside/outside residue distribution, homology modeling validation 519
Intercalation complexes, DNA-drug interactions 59—60
Interface definition language (IDL), Common Object Request Broker Architecture (CORBA) 178
InterPro initiative, CATH domain structure database 248
Introns, ribozyme structure 63—64
Investigational new drugs (INDs), bioinformatics 477
Ion pairing, tertiary protein structure 30
Ising models, domain identification 377
Isomorphous substitution, high-throughput crystallographic analysis, macromolecular structures 77
IUCr review, macromolecular Crystallographic Information File (mmCIF) 164—165
JPred2 server, one-dimensional secondary structure prediction, solvent accessibility models 563
Kernigan — Lin heuristic, domain identification, second generation assignment algorithms 372—377
Kinases, drug bioinformatics, target druggability 479—480
KINEMAGE software, macromolecular visualization 138
Knowledge-based potentials, docking and ligand design, scoring functions 457
Knowledge-based potentials, homology modeling, loop regions 514
Knowledge-based potentials, homology modeling, side-chain conformations 515—516
L-amino acids, protein structure, error estimation and precision 290—292
Landscape models, docking and ligand design 467
Laplacian operator, electrostatic interactions, Poisson — Boltzmann equation (PBE), finite difference discretization 433
Lattice representation, ab initio fold prediction, polypeptide chains 547
Legacy data, Protein Data Bank (PDB) uniformity protocols 187—189
Lennard — Jones functions, docking and ligand design, Van der Waals radii 459
Ligand nomenclature, Protein Data Bank (PDB) data validation and annotation 186
Ligand-protein interactions, protein function identification 391—392
Ligand-protein interactions, ReliBase data source 224
Ligands, design principles, ADME properties 468
Ligands, design principles, combinatorial calculation 461
Ligands, design principles, complex formation flow chart 450—454
Ligands, design principles, computer-aided drug design (CADD) 444—450
Ligands, design principles, computer-aided drug design (CADD), analog-based design 444—445
Ligands, design principles, computer-aided drug design (CADD), structure-based design 445—449
Ligands, design principles, computer-aided drug design (CADD), virtual library design 449—450
Ligands, design principles, database organization 466—467
Ligands, design principles, de novo design cycles 443
Ligands, design principles, experimental conditions 454—455
Ligands, design principles, free energies and energy binding 450
Ligands, design principles, future scoring techniques 465—466
Ligands, design principles, landscape models 467
Ligands, design principles, macromolecular docking 467
Ligands, design principles, molecular mechanics scoring parametrization 457—461
Ligands, design principles, molecular mechanics scoring parametrization, charge representation 457—459
Ligands, design principles, molecular mechanics scoring parametrization, solvent representation 459—461
Ligands, design principles, molecular mechanics scoring parametrization, van der Waals radii 459
Ligands, design principles, pharmacogenetics 468
Ligands, design principles, research background 441—443
Ligands, design principles, scoring functions 456—457
Ligands, design principles, scoring functions, empirical methods 457
Ligands, design principles, scoring functions, first principles methods 456
Ligands, design principles, scoring functions, knowledge-based potentials 457
Ligands, design principles, scoring functions, semiempirical methods 456
Ligands, design principles, solvation/hydration effects 454 456
Ligands, design principles, success rates 465
Ligands, design principles, testing procedures 462—465
Ligands, design principles, testing procedures, complex reassembly 462—464
Ligands, design principles, testing procedures, failure testing 464—465
Ligands, design principles, testing procedures, virtual screening 464
Line Drawing System 1 (LDS1), macromolecular visualization 137
Linear interaction energy (LIE), docking and ligand design, semiempirical scoring functions 456
Linear polymer theory, amino acid sequence 16—17
Lipid modification, tertiary protein structure 30
List server, Protein Data Bank (PDB) 194
LiveBench server, one-dimensional secondary structure prediction, evaluation of programs 568
Loop regions, homology modeling 508—510 513—514
Loop regions, homology modeling, model optimization 516—518
Loop regions, mismaiched/bulged RNA 62—63
Loop regions, secondary protein structure 24—28
Loop-directive, macromolecular Crystallographic Information File (mmCIF) 166—167
Lorentz — Berthelot model, docking and ligand design, Van der Waals radii 459
LUDI scoring function, docking and ligand design 457
Luzzati plot, deposited structures, errors in 286
Luzzati plot, x-ray crystallography models, average positional error 281
Macromolecular Crystallographic Information File (mmCIF), alternative data dictionaries 175
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management 164—175
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, atomic positions 173—175
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, dictionary content 170—175
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, molecular entities 171
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, polymer and non-polymer entities 172—173
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, semantic elements 169—170
Macromolecular Crystallographic Information File (mmCIF), dictionary-based data management, syntax structure 165—169
Macromolecular Crystallographic Information File (mmCIF), Nucleic Acid Database (NDB) 199
Macromolecular Crystallographic Information File (mmCIF), Nucleic Acid Database (NDB), validation procedures 201—202
Macromolecular Crystallographic Information File (mmCIF), Protein Data Bank (PDB) data acquisition 182—184
Macromolecular Crystallographic Information File (mmCIF), Protein Data Bank (PDB) data acquisition, uniformity protocols 188—189
MacroMolecular Database (MMDB), sequence, literature and genome information 221—222
MAcromolecular Exchange Input Tool (MAXIT), Nucleic Acid Database (NDB) validation 201—202
MAcromolecular Exchange Input Tool (MAXIT), Protein Data Bank (PDB) data, acquisition 182
Macromolecular Motions Database (MolMovDB), content and protocol 226—227
Macromolecular Structure, data flow 215 218
Macromolecular Structure, Database/European Bioinformatics Institute (MSD-EBI), Protein Data Bank (PDB) data deposition 187
Macromolecular Structure, Database/European Bioinformatics Institute (MSD-EBI), Protein Quaternary Structure (PQS) resource 222—223
Macromolecular Structure, electrostatic interactions, Poisson — Boltzmann equation (PBE) 435—436
Macromolecular Structure, high-throughput crystallographic analysis, automation issues 82—83
Macromolecular Structure, high-throughput crystallographic analysis, data analysis techniques 76—77
Macromolecular Structure, high-throughput crystallographic analysis, density modification 78
Macromolecular Structure, high-throughput crystallographic analysis, disorder 83
Macromolecular Structure, high-throughput crystallographic analysis, heavy atom location and computation 77—78
Macromolecular Structure, high-throughput crystallographic analysis, map interpretation 79—81
Macromolecular Structure, high-throughput crystallographic analysis, molecular replacement 78—79
Macromolecular Structure, high-throughput crystallographic analysis, noncrystallographic symmetry 82—83
Macromolecular Structure, high-throughput crystallographic analysis, principles 76
Macromolecular Structure, high-throughput crystallographic analysis, refinement methods 81—82
Macromolecular Structure, high-throughput crystallographic analysis, research background 75
Macromolecular Structure, high-throughput crystallographic analysis, validation 82
Macromolecular Structure, macromolecular docking 467
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, bioinformatics applications 91—94
| Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, cell-free protein production 104—105
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, concerted approaches 106
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, experimental protocols 91
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, future research issues 104—106
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, model validation 102—103
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics 104
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, physical principles 90—91
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, protein sampling 96—97
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, protein structure 97—102
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, protocols 99—102
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, research background 89
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, screening methods 94—96
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, stereo array isotope labeling (SAIL) 105—106
Macromolecular Structure, nuclear magnetic resonance (NMR) spectroscopy, vs. x-ray crystallography 90
Macromolecular Structure, primary data sources 215 218
Macromolecular Structure, primary data sources, Biological Macromolecule Crystallization Database (BMCD) 218—219
Macromolecular Structure, primary data sources, Cambridge Structural Database (CSD) 219—220
Macromolecular Structure, primary data sources, future structure information 220
Macromolecular Structure, visualization techniques, historical background 135—144
Macromolecular Structure, visualization techniques, software characteristics 135—144
Macromolecular Structure, visualization techniques, sources for 215 217
Macromolecular Structure, visualization techniques, table of software options 150—156
Macromolecular Structure, visualization techniques, tool kits 148—149
Macromolecular Structure, visualization techniques, web-based software 145—148
Mage/Probe system, all-atom contact analysis 314—316
MAID program, high-throughput crystallographic analysis, electron density map interpretation 80
Manual fitting techniques, electron cryomicroscopy/x-ray crystallography procedures 126—127
MAP kinases, drug bioinformatics, target validation 486—487
Maximum-likelihood estimates, high-throughput crystallographic analysis, heavy atom location 78
Maximum-likelihood estimates, high-throughput crystallographic analysis, molecular replacement 79
Maximum-likelihood estimates, high-throughput crystallographic analysis, refinement techniques 81—82
MC-Annotate, nucleic acid structures, error estimation and precision 295
MDB dictionary, format and content 175
MDD see "Yeast mevalonate-5-diphosphate decarboxylase (MDD)"
Membrane-bound proteins, biochemical classification 32—33
Membrane-bound proteins, electron cryomicroscopy, three-dimensional crystalline arrays 121
Membrane-bound proteins, one-dimensional secondary structure prediction, evalution of techniques 571
Membrane-bound proteins, one-dimensional secondary structure prediction, transmembrane helix prediction 563—566
Membrane-bound proteins, structural bioinformatics 7
Membrane-bound proteins, structural comparison and alignment 328—329
Membrane-bound proteins, structural genomics 606—607
MEMSAT program, one-dimensional secondary structure prediction, transmembrane helix prediction 565—566
Merohedral twinning, high-throughput crystallographic analysis, macromolecular structures 77
Met conformations, all-atom contact analysis 311—316
Metalloprotein Database and Browser (MDB), data content 225—226
Metalloproteins, data sources 225—226
Metropolis criterion, docking and ligand orientation 447—448
Metropolis Monte Carlo simulated annealing, ab initio fold prediction 548—549
Minimized protein density, stereo array isotope labeling (SAIL) 105—106
Minimum contact density profile, domain identification, second generation assignment algorithms 372—377
Mining Minima, docking and ligand orientation 447—448
MIPS database, protein-protein interaction prediction 417
Mirror sites, Nucleic Acid Database (NDB) 205—206
Mirror sites, Protein Data Bank (PDB) 194—195
Mirrortree method, protein-protein interaction prediction, sequence-based computation 419—421
Mismatched RNA, structural characteristics 62—63
Mjo577 genome, protein function identification 400—401
MLPHARE program, high-throughput crystallographic analysis, heavy atom location 78
Modified image electrostatic approximation (MIMEL), docking and ligand design 465—466
MODPIPE system, homology modeling, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study 600—601
Molecular Biology Toolkit (MBT), macromolecular visualization 149
Molecular dynamics, docking and ligand orientation, complex formation 452—454
Molecular dynamics, homology model optimization 518
Molecular dynamics, NMR spectroscopy 104
Molecular entities, macromolecular Crystallographic Information File (mmCIF) 171
Molecular Information Agent (MIA), multiple resource integration 229—231
Molecular Information Agent (MIA), Protein Data Bank (PDB) architecture 190—191
Molecular interactions, tertiary protein structure 29—30
Molecular Interactive Collaborative Environment (MICE), macromolecular visualization 145—148
Molecular mechanics scoring functions, ab initio fold prediction, potentials categories 547—548
Molecular mechanics scoring functions, docking and ligand design 457—461
Molecular mechanics scoring functions, docking and ligand design, charge representation 457—459
Molecular mechanics scoring functions, docking and ligand design, solvent representation 459—461
Molecular mechanics scoring functions, docking and ligand design, van der Waals radii 459
Molecular Modeling Toolkit (MMTK), macromolecular visualization 149
Molecular modeling, structural bioinformatics 4—6
Molecular recognition, protein function identification 399
Molecular replacement, high-throughput crystallographic analysis 78—79
Molecular structures, structural bioinformatics, database storage 9
MolProbity subsite, all-atom contact analysis 316—317
MolScript software, CATH domain structure database 250—252
MolScript software, macromolecular visualization 143
Monte Carlo optimization, ab initio fold prediction 548—549
Monte Carlo optimization, docking and ligand orientation 447—448
Monte Carlo optimization, docking and ligand orientation, complex formation 452—454
Monte Carlo optimization, multiple structure alignments 329— 330
Morph Server software, Macromolecular Motions Database (MolMovDB) 227
Motifs, protein function identification 397—399
Motifs, tertiary protein structure 29
Motor proteins, electron cryomicroscopy, protein dynamics 124—125
mRNA sequencing, bioinformatics and 3
Multifunctional proteins, identification 388
Multilevel solvers, electrostatic interactions, Poisson — Boltzmann equation (PBE) 435
Multiple polypeptide chains, quaternary protein structure 33—36
Multiple sequence alignment, fold recognition, protein families 529—531
Multiple sequence alignment, homology modeling 512—513
Multiple sequence alignment, homology modeling, backbone generation 513
Multiple structure alignments, CATH domain structure database 257
Multiple structure alignments, domain identification 379—380
Multiple structure alignments, evolutionary information, protein-protein interaction prediction 410—411
Multiple structure alignments, Monte Carlo optimization 329—330
Multiple structure alignments, tree determinant residues 413
Multiwavelength Anomalous Diffraction (MAD), high-throughput crystallographic analysis, macromolecular structures 77
Multiwavelength Anomalous Diffraction (MAD), structural bioinformatics 8
MySQL database system, Metalloprotein Database and Browser (MDB) 226
NAContacts script, all-atom contacts 313—316
NAD binding domain, protein function identification 393—394
NASA, Protein Crystal Growth Archive 218—219
National Center for Biotechnology Information (NCB1, MacroMolecular Database (MMDB) 221—222
National Institute of General Medical Sciences (N1GMS) Protein Structure Initiative (PSI), structural genomics pilot programs 593—597
Netscape LDAP server, Protein Data Bank (PDB) architecture 190—191
Neural networks, one-dimensional secondary structure prediction 559—562
Neural networks, one-dimensional secondary structure prediction, solvent accessibility models 563
Neural networks, protein-protein interaction prediction 415—416
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program 597—604
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, biomedical implications 604
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, evolutionary mechanisms 601
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, homology modeling 600—601
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, homology modeling, MDD/HSK structures 601
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, progress summary 604—605
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, sample preparation and characterization 597—599
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, structural overview 599—600
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, target selection 597 601—604
New York Structural Genomics Research Consortium (NYSGRC), structural genomics pilot program, x-ray structure determination 599
Newton techniques, electrostatic interactions, Poisson — Boltzmann equation (PBE) 432—435
Nitrogen-15, macromolecular structure, NMR spectroscopy 90—91
Nitrogen-15, macromolecular structure, screening methods 94—96
NMR-STAR, macromolecular structure 93—94
NMRPipc program, protein structure, NMR spectroscopy 100—102
Noise issues, structural bioinformatics 7
Non-polymer entities, macromolecular Crystallographic Information File (mmCIF) 172—173
Noncovalent interactions, docking and ligand design 451—454
Noncrystallographic symmetry, high-throughput crystallographic analysis 82—83
Nonenzyme classification, protein function identification 386—388
Nonlinearity, structural bioinformatics 6
Nonredundant data sources, ASTRAL compendium 220—221
Normality indices, homology modeling validation 519
NP problems, structure comparison and alignment 322—327
NSSP system, one-dimensional secondary structure prediction 561—562
NuCheck software, Nucleic Acid Database (NDB) validation 201—202
NuCheck software, nucleic acid structures, error estimation and precision 294—295
Nuclear magnetic resonance (NMR) spectroscopy, all-atom contact analysis 316
Nuclear magnetic resonance (NMR) spectroscopy, electron cryomicroscopy and 125—127
Nuclear magnetic resonance (NMR) spectroscopy, error estimates 282—284
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, bioinformatics applications 91—94
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, cell-free protein production 104—105
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, concerted approaches 106
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, experimental protocols 91
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, future research issues 104—106
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, model validation 102—103
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