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| Ïîèñê ïî óêàçàòåëÿì |
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| Bourne P.E., Weissig H. — Structural bioinformatics |
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| Ïðåäìåòíûé óêàçàòåëü |
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, molecular dynamics 104
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, physical principles 90—91
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, protein sampling 96—97
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, protein structure 97—102
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, protocols 99—102
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, research background 89
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, screening methods 94—96
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, stereo array isotope labeling (SAIL) 105—106
Nuclear magnetic resonance (NMR) spectroscopy, macromolecular structure, vs. x-ray crystallography 90
Nuclear magnetic resonance (NMR) spectroscopy, Protein Data Bank (PDB) data acquisition 184
Nuclear magnetic resonance (NMR) spectroscopy, quality assurance 273—274
Nuclear magnetic resonance (NMR) spectroscopy, secondary structure assignment for 351
Nuclear magnetic resonance (NMR) spectroscopy, secondary structure assignment for, continuous Dictionary of Secondary Structure of Proteins (DSSPcont) 355—356
Nuclear magnetic resonance (NMR) spectroscopy, structural bioinformatics 8—9
Nuclear Overhouser Effect spectroscopy (NOESY), error estimation and precision, NMR models 283—284
Nuclear Overhouser Effect spectroscopy (NOESY), macromolecular structure, NMR spectroscopy 91
Nuclear Overhouser Effect spectroscopy (NOESY), macromolecular structure, protein structural analysis 97—98
Nuclear Overhouser Effect spectroscopy (NOESY), protein structure, assignment and structure calculation 101—102
Nuclear Overhouser Effect spectroscopy (NOESY), protein structure, NMR spectroscopy 100—102
Nuclear Overhouser Effect spectroscopy (NOESY), protein structure, validation 103
Nuclear Overhouser Effect spectroscopy (NOESY), quality assurance 273—274
Nucleic Acid Database (NDB), applications 206—210
Nucleic Acid Database (NDB), Archives page 205—206
Nucleic Acid Database (NDB), Atlas reports 205—206
Nucleic Acid Database (NDB), data distribution 204—206
Nucleic Acid Database (NDB), data distribution, mirror sites 205—206
Nucleic Acid Database (NDB), data distribution, outreach programs 206
Nucleic Acid Database (NDB), data validation and processing 201—202
Nucleic Acid Database (NDB), future research issues 210—211
Nucleic Acid Database (NDB), historical background 199
Nucleic Acid Database (NDB), information content 200—201
Nucleic Acid Database (NDB), macromolecular structure, validation 102—103
Nucleic Acid Database (NDB), Protein Data Bank (PDB) architecture 191
Nucleic Acid Database (NDB), query capabilities 202—204
Nucleic acid structures, chemical structure 42—45
Nucleic acid structures, DNA duplexes 55—59
Nucleic acid structures, DNA quadruplexes 60
Nucleic acid structures, drug complexes 59—60
Nucleic acid structures, error estimation and precision 294—295
Nucleic acid structures, ribosome 64—67
Nucleic acid structures, ribozymes 63—64
Nucleic acid structures, RNA duplexes 60—62
Nucleic acid structures, RNA mismatches and bulges 62—63
Nucleic acid structures, structural bioinformatics 7
Nucleic acid structures, transfer RNA (tRNA) 63
Nucleic-acid crystal structures, all-atom contacts 311—316
Nucleosides, nucleic acid chemical structure 42—45
Nucleotides, nucleic acid chemical structure 42—45
O software, high-throughput crystallographic analysis, electron density map interpretation 80
O software, macromolecular visualization 136 141
Object Management Group (OMG), application program interface (API) protocols 178
Object Management Group (OMG), XML format and protocols 176—178
Oligonucleotides, DNA structure 41—42
Oligonucleotides, Nucleic Acid Database (NDB) information 200—201
One-dimensional models, Cambridge Structural Database (CSD) sources 219
One-dimensional models, secondary structures, emerging and future technologies 571—574
One-dimensional models, secondary structures, evaluation of prediction techniques 566—568
One-dimensional models, secondary structures, practical applications 568—571
One-dimensional models, secondary structures, prediction techniques 558—562
One-dimensional models, secondary structures, programs and public servers 566
One-dimensional models, secondary structures, solvent accessibility prediction 562—563
One-dimensional models, secondary structures, theoretical background 557—558
One-dimensional models, secondary structures, transmembrane helix prediction 563—566
One-window free energy grid (OWFEG), docking and ligand design, rank ordering 463
Open reading frame (ORF), protein function identification, genomic structure 400—401
Optical resolution, electron cryomicroscopy 116—119
Oracle 8i relational database, CATH domain structure data 261—263
Orientation, docking molecule design 445
Orientation, ligand design 447—448
Outreach activities, Nucleic Acid Database (NDB) 206
Outreach activities, Protein Data Bank (PDB) 194—195
Overlaps, all-atom contact analysis 305—307
P-Curve assignment scheme, automatic assignment comparisons 347—349
P-Curve assignment scheme, secondary protein structure 345—346
P-loop NTP hydrolase fold, protein function identification 393—394
Pairwise structure comparison and alignment, high-throughput crystallographic analysis 416
Pairwise structure comparison and alignment, protocols and methods 322—327
Parallel computing, electron cryomicroscopy 128—129
Parallel computing, electrostatic interactions, Poisson — Boltzmann equation (PBE) 435—436
Parallel structures,  sheets, secondary protein structure 24
PartsList database, content and protocol 227—228
Pattern recognition, electron cryomicroscopy and 127—128
Pattern recognition, one-dimensional secondary structure models, theoretical background 558—562
Patterson-based techniques, high-throughput crystallographic analysis, heavy atom location 77—78
Patterson-Correlation (PC) refinement, high-throughput crystallographic analysis, molecular replacement 79
PDB see "Protein Data Bank (PDB)"
PDB identification (PDBid), establishment of 181
PDBREPORT database, homology modeling, backbone generation 513
PDBREPORT database, WHATCHECK results 298
PDBselect, ASTRAL compendium 221
PDBsum website, quality assurance information 296—297
Peak assignment, protein structure, NMR spectroscopy 101
Peptides, bonds, amino acid sequence 17—20
Peptides, structural studies, validation 102—103
Perl CGI scripts, Protein Data Bank (PDB) 190—191
Pharmaceutical models, drug bioinformatics 477—479
Pharmacogenetics, docking and ligand design 468
Pharmacophores, analog-based design 444
Phase problem, structure-based drug design (SBDD) 489—490
PHD program, one-dimensional secondary structure prediction, error detection 570
PHD program, one-dimensional secondary structure prediction, limits of 560—562
PHD program, one-dimensional secondary structure prediction, solvent accessibility models 563
PHD program, one-dimensional secondary structure prediction, transmembrane helix prediction 566
Phosphomevalonate kinases (PMK), structural genomics, homology modeling 601
Phosphomevalonate kinases (PMK), structural genomics, target selection 602—604
Phosphorus-31, macromolecular structure, NMR spectroscopy 90—91
Phylogenetic profiles, fold recognition, theoretical background 526
Phylogenetic profiles, protein-protein interaction prediction, genomic-based computation 417
Phylogenetic profiles, protein-protein interaction prediction, sequence-based computation 419—421
Physics principles, fold recognition, algorithm comparison and assessment 539—540
Physics principles, fold recognition, force field simulation and threading 533
Physics principles, fold recognition, theoretical background 526
Physics principles, fold recognition, threading approximation 533—536
Physics principles, fold recognition, threading errors 535 537—539
Physics principles, structural bioinformatics 7
Point charge models, docking and ligand design, molecular mechanics scoring functions 457—459
Point charge models, solvent representation 459—461
Poisson equation, electrostatic interactions 428—430
Poisson — Boltzmann equation (PBE), docking and ligand design, solvent representation 460—461
Poisson — Boltzmann equation (PBE), electrostatic interactions 428—435
Poisson — Boltzmann equation (PBE), electrostatic interactions, energy derivations 430—431
Poisson — Boltzmann equation (PBE), electrostatic interactions, equation elements 428—430
Poisson — Boltzmann equation (PBE), electrostatic interactions, force elements 431—432
Poisson — Boltzmann equation (PBE), electrostatic interactions, multilevel solvers 435
Poisson — Boltzmann equation (PBE), electrostatic interactions, numerical solution 432—435
Poisson — Boltzmann equation (PBE), electrostatic interactions, numerical solution, adaptive finite element discretization 433—435
Poisson — Boltzmann equation (PBE), electrostatic interactions, numerical solution, finite difference discretization 432—433
Polar amino acids, side chain sequence 17
Polar amino acids, tertiary protein structure, hydrophobic effect 29—30
Polymer entities, macromolecular Crystallographic Information File (mmCIF) 172—173
Polynucleotide chains, nucleic acid chemical structure 43—45
Polypeptide chains, ab initio fold prediction 546—547
Polypeptide chains, domain identification 365—367
Polypeptide chains, evolutionary mechanisms 239
Polypeptide chains, quaternary protein structure 33—36
Population statistics, CATH domain structure database, fold architectures 263—264
Population statistics, CATH domain structure database, superfamilies and families 264—267
POSSUM algorithm, CATH domain structure database, Graphical Method for Identifying Folds (GRATH) 256—257
Potentials categories, ab initio fold prediction 547—548
Potentials of mean force (PMF) see also "Force field evaluation"
Potentials of mean force (PMF), docking and ligand design, rank ordering of energies 463
Potentials of mean force (PMF), docking and ligand design, scoring functions 457
Potentials of mean force (PMF), docking and ligand design, solvent representation 460—461
Potentials of mean force (PMF), told recognition, force fields and threading simulation 533
PREDATOR system, one-dimensional secondary structure prediction 561—562
Prediction techniques, ab initio fold prediction, applications 549—551
Prediction techniques, ab initio fold prediction, applications, genome annotation 549—550
Prediction techniques, ab initio fold prediction, applications, structural genomics 550—551
Prediction techniques, ab initio fold prediction, future research 551—552
Prediction techniques, ab initio fold prediction, polypeptide chain representations 546—547
| Prediction techniques, ab initio fold prediction, potentials categories 547—548
Prediction techniques, ab initio fold prediction, search methods 548—549
Prediction techniques, data sources 228—229
Prediction techniques, fold recognition 525
Prediction techniques, one-dimensional secondary structure models, emerging and future technologies 571—574
Prediction techniques, one-dimensional secondary structure models, evaluation of prediction techniques 566—568
Prediction techniques, one-dimensional secondary structure models, practical applications 568—571
Prediction techniques, one-dimensional secondary structure models, prediction techniques 558—562
Prediction techniques, one-dimensional secondary structure models, programs and public servers 566
Prediction techniques, one-dimensional secondary structure models, solvent accessibility prediction 562—563
Prediction techniques, one-dimensional secondary structure models, theoretical background 557—558
Prediction techniques, one-dimensional secondary structure models, transmembrane helix prediction 563—566
Prediction techniques, protein function identification, ab initio methods 396—397
Prediction techniques, protein-protein interaction, evolutionary information, coevolution 411
Prediction techniques, protein-protein interaction, evolutionary information, conservation of positions 410
Prediction techniques, protein-protein interaction, evolutionary information, family-dependent conservation 411
Prediction techniques, protein-protein interaction, evolutionary information, future applications 421—422
Prediction techniques, protein-protein interaction, evolutionary information, interaction partners 416—421
Prediction techniques, protein-protein interaction, evolutionary information, interaction partners, genomic-based computation 417—418
Prediction techniques, protein-protein interaction, evolutionary information, interaction partners, high-throughput applications 416
Prediction techniques, protein-protein interaction, evolutionary information, interaction partners, protein databases and collections 416—417
Prediction techniques, protein-protein interaction, evolutionary information, interaction partners, sequence-based computation 418—421
Prediction techniques, protein-protein interaction, evolutionary information, interaction regions 411—416
Prediction techniques, protein-protein interaction, evolutionary information, interaction regions, hybrid methods 413—416
Prediction techniques, protein-protein interaction, evolutionary information, interaction regions, research background 409—410
Prediction techniques, protein-protein interaction, evolutionary information, interaction regions, sequence-based methods 413
Prediction techniques, protein-protein interaction, evolutionary information, interaction regions, structure-based methods 411—412
Prediction techniques, secondary protein structure, structure assignment 340
Prediction techniques, structural bioinformatics 10
Probabilistic modeling, structural bioinformatics 4—6
Probe software, all-atom contact analysis 305—307
PROCHECK program, ASTRAL compendium 221
PROCHECK program, error estimation and precision 296
PROCHECK program, PDBsum website summaries 296—297
PROCHECK program, Protein Data Bank (PDB) data validation and annotation 186
PROCHECK program, protein structure, error estimation and precision 291—292
PROCHECK program, protein structure, validation 102—103
Profile-based techniques, CATH domain structure database, sequence-based homologue protocols 253—255
Profile-profile alignment tools, fold recognition, divergent evolution 524
PROFphd, one-dimensional secondary structure prediction, solvent accessibility models 563
Proline, cyclic side chain sequence 17
Proline, peptide bond structure 19—20
ProNet database, protein-protein interaction prediction 417
Propeller twist, base pair geometry 46—47
Propeller twist, DNA duplexes 56—59
Property Object Model (POM) data management system, Protein Data Bank (PDB) architecture 190—191
PROSITE motifs, CATH domain structure database, Dictionary of Homologous Superfamilies (DHS) 259—260
Proteases, drug bioinformatics, target druggability 480
Protein Data Bank (PDB) data 194
Protein Data Bank (PDB) data acquisition 182
Protein Data Bank (PDB), added-value philosophy 217
Protein Data Bank (PDB), all atom contact analysis 311—316
Protein Data Bank (PDB), data access issues 189—194
Protein Data Bank (PDB), data access issues, application web access 193—194
Protein Data Bank (PDB), data access issues, database architecture 190—191
Protein Data Bank (PDB), data access issues, ftp access 194
Protein Data Bank (PDB), data access issues, user web access 191—193
Protein Data Bank (PDB), data acquisition and processing 182—189
Protein Data Bank (PDB), data acquisition and processing, content characteristics 184
Protein Data Bank (PDB), data acquisition and processing, deposition sites 187
Protein Data Bank (PDB), data acquisition and processing, statistics 187
Protein Data Bank (PDB), data acquisition and processing, uniformity protocols 187—189
Protein Data Bank (PDB), data acquisition and processing, validation and annotation 184—186
Protein Data Bank (PDB), error estimation and precision, Archive of Obsolete PDB entries 284—286
Protein Data Bank (PDB), exchange dictionary 175
Protein Data Bank (PDB), format 161—164
Protein Data Bank (PDB), future applications 195—196
Protein Data Bank (PDB), Help desk 194
Protein Data Bank (PDB), high-resolution techniques 6
Protein Data Bank (PDB), high-throughput crystallographic analysis 76
Protein Data Bank (PDB), historical background 181—182
Protein Data Bank (PDB), interoperability beyond cross-links 231
Protein Data Bank (PDB), macromolecular structure, NMR spectroscopy 92—94
Protein Data Bank (PDB), macromolecular structure, validation 102—103
Protein Data Bank (PDB), multiple resource integration 229—231
Protein Data Bank (PDB), outreach activities 194—195
Protein Data Bank (PDB), primary data sources 215 218
Protein Data Bank (PDB), primary data sources, Biological Macromolecule Crystallization Database (BMCD) 218—219
Protein Data Bank (PDB), primary data sources, Cambridge Structural Database (CSD) 219—220
Protein Data Bank (PDB), primary data sources, future structure information 220
Protein Data Bank (PDB), protein function identification 391—392
Protein Data Bank (PDB), quality assurance, NMR modeling 274
Protein Data Bank (PDB), secondary data sources 215—216 218
Protein Data Bank (PDB), secondary data sources, ASTRAL compendium, sequence and structure relationships 220—221
Protein Data Bank (PDB), secondary data sources, Derived Secondary Structure of Proteins (DSSP) 222
Protein Data Bank (PDB), secondary data sources, HIV Proteases resource (HIVpr) 225
Protein Data Bank (PDB), secondary data sources, MacroMolecular DataBase (MMDB) 221—222
Protein Data Bank (PDB), secondary data sources, Macromolecular Motions Database (MolMovDB) 226—227
Protein Data Bank (PDB), secondary data sources, Metalloprotein Database and Browser (MDB) 225—226
Protein Data Bank (PDB), secondary data sources, PartsList dynamic fold comparisons 227—228
Protein Data Bank (PDB), secondary data sources, Protein Kinase Resource (PKR) 224—225
Protein Data Bank (PDB), secondary data sources, Protein Quaternary Structure (PQS) 222—223
Protein Data Bank (PDB), secondary data sources, ReliBase, protein ligand interaction 224
Protein Data Bank (PDB), secondary data sources, Swiss-Model automated comparative modeling 228
Protein Data Bank (PDB), secondary data sources, targets and prediction methods 228—229
Protein Data Bank (PDB), structural bioinformatics 5
Protein Data Bank (PDB), structural genomics 231—232 501
Protein Data Bank (PDB), tertiary protein structure 31
Protein dynamics, electron cryomicroscopy 124—125
Protein Explorer web-based visualization techniques 147—148
Protein families, data resources 224—229
Protein families, data resources, HIV proteases resource (HIVpr) 225
Protein families, data resources, Macromolecular Motions Database (MolMvDB) 226—227
Protein families, data resources, Metalloprotein Database and Browser (MDB) 225—226
Protein families, data resources, PartsList 227—228
Protein families, data resources, Protein Kinase Resource (PKR) 224—225
Protein families, data resources, Swiss-Model 226
Protein families, data resources, targets and prediction methods 226—227
Protein folding see also "Fold recognition"
Protein folding, biochemical classification 31—33
Protein folding, CATH domain structure database, Graphical Method for Identifying Folds (GRATH) 256—257
Protein folding, CATH domain structure database, population statistics 263—264
Protein folding, CATH domain structure database, Sequence Structure Alignment Program (SSAP) protocols 255—256
Protein folding, CATH domain structure database, superfamily and family population statistics 264—267
Protein folding, Critical Assessment for Structure Prediction (CASP), comparative modeling 502—503
Protein folding, Critical Assessment for Structure Prediction (CASP), fold recognition 503
Protein folding, Critical Assessment for Structure Prediction (CASP), novel fold recognition 503—504
Protein folding, Critical Assessment for Structure Prediction (CASP), research background 499—501
Protein folding, Critical Assessment for Structure Prediction (CASP), summary of progress 501—502
Protein folding, data sources, PartsList database 227—228
Protein folding, evolutionary mechanisms 238
Protein folding, protein function identification 392
Protein folding, protein function identification, enzyme function and 393—394
Protein folding, quaternary protein structure 34—36
Protein folding, SCOP hierarchical classification 239 241
Protein folding, space mapping, structure comparison and alignment 330—332
Protein folding, structural classification 33
Protein folding, tertiary protein structure 29
Protein Kinase Resource (PKR), data content 224—225
Protein kinases, structural comparison and alignment 327—328
Protein production and labeling, macromolecular structure, NMR spectroscopy 96—97
Protein Quaternary Structure (PQS), database, secondary data sources 222—223
Protein structure see also "Domains" "Homology
Protein structure, amino acid sequence 16—20
Protein structure, amino acid sequence, amino acid structures 16—17
Protein structure, amino acid sequence, peptide bond 17—20
Protein structure, classification resources 215—216
Protein structure, classification resources, domain identification 370
Protein structure, comparison and alignment 324—325
Protein structure, electrostatic interactions 426—427
Protein structure, error estimation and precision 289—294
Protein structure, error estimation and precision, C-alpha only structures 294
Protein structure, error estimation and precision, Ramachandran plot 289—292
Protein structure, error estimation and precision, side-chain torsion angles 292—294
Protein structure, evolution 237—239
Protein structure, evolution, coevolution 411
Protein structure, evolution, conservation of positions 410
Protein structure, evolution, enzymatic catalysis 238—239
Protein structure, evolution, family-dependent conservation 411
Protein structure, evolution, fold evolution 238
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