Bourne P.E., Weissig H. — Structural bioinformatics :: Электронная библиотека попечительского совета мехмата МГУ

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Bourne P.E., Weissig H. — Structural bioinformatics

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Название: Structural bioinformatics

Авторы: Bourne P.E., Weissig H.

Аннотация:

This book provides a basic understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics. The reader emerges with the ability to make effective use of protein, DNA, RNA, carbohydrate, and complex structures to better understand biological function. Moreover, it draws a clear connection between structural studies and the rational design of new therapies.

Язык:

Рубрика: Computer science/Биоинформатика/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2003

Количество страниц: 649

Добавлена в каталог: 10.11.2005

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID

Предметный указатель

Protein structure, evolution, structural comparisons      239
Protein structure, fold recognition, current applications      523—525
Protein structure, fold recognition, threading algorithms      534—535
Protein structure, function derivation, ab initio prediction      396—397
Protein structure, function derivation, analogues      395—396
Protein structure, function derivation, assignment protocols      396—402
Protein structure, function derivation, database classification      388—390
Protein structure, function derivation, definitions      386
Protein structure, function derivation, enzyme function      393
Protein structure, function derivation, enzyme/nonenzyme classification      386—388
Protein structure, function derivation, Fuzzy Functional Forms (FFF) algorithm      398—399
Protein structure, function derivation, gene ontologies      388 391
Protein structure, function derivation, genomic applications      400—402
Protein structure, function derivation, genomic applications, IMPase      402
Protein structure, function derivation, genomic applications, Mj0577—putative Atp molecular switch      400—401
Protein structure, function derivation, genomic applications, YcaC-bacterial hydrolase      401—402
Protein structure, function derivation, homologous families      393 395
Protein structure, function derivation, molecular recognition      399
Protein structure, function derivation, multifunctional proteins      388
Protein structure, function derivation, protein fold and      393—394
Protein structure, function derivation, protein-ligand complexes      391—392
Protein structure, function derivation, research background      385—386
Protein structure, function derivation, RIGOR tool      399
Protein structure, function derivation, side chain patterns      399
Protein structure, function derivation, SITE and Site-Match      398
Protein structure, function derivation, SPASM tool      399
Protein structure, function derivation, structural comparisons      397
Protein structure, function derivation, structural motifs      397—399
Protein structure, function derivation, TESS algorithm      398
Protein structure, function derivation, three-dimensional structures      391—392
Protein structure, internet sources      36
Protein structure, NMR spectroscopy, protocols for      99—102
Protein structure, quality assurance, error estimation and precision      275—296
Protein structure, quality assurance, error estimation and precision, deposited structures      284—296
Protein structure, quality assurance, error estimation and precision, NMR spectroscopic errors      282—284
Protein structure, quality assurance, error estimation and precision, x-ray crystal lographic errors      275—282
Protein structure, quality assurance, NMR spectroscopy models      273—274
Protein structure, quality assurance, research background      271—272
Protein structure, quality assurance, software      296
Protein structure, quality assurance, web information sources      296—298
Protein structure, quality assurance, x-ray crystallography models      272—273
Protein structure, quaternary structure, multiple polypeptide chains      33—36
Protein structure, research applications      15—16
Protein structure, SCOP database, applications      237
Protein structure, SCOP database, classification      240—241
Protein structure, SCOP database, families classification      242
Protein structure, SCOP database, fold classification      241
Protein structure, SCOP database, hierarchies      239—240 243—244
Protein structure, SCOP database, organization and capabilities      242—244
Protein structure, SCOP database, superfamilies classification      242
Protein structure, SCOP database, user interface      244—246
Protein structure, secondary structure, $\alpha$ -helices      22—24
Protein structure, secondary structure, $\beta$ sheets      24
Protein structure, secondary structure, local three-dimensional model      20—28
Protein structure, secondary structure, loops and coils      24—28
Protein structure, structural bioinformatics      7
Protein structure, tertiary structure, biological fold classification      31—33
Protein structure, tertiary structure, domains and motifs      29
Protein structure, tertiary structure, fold space and evolution      30—31
Protein structure, tertiary structure, fold structure classification      33
Protein structure, tertiary structure, global three-dimensional structure      28—33
Protein structure, tertiary structure, modifications      30
Protein structure, tertiary structure, molecular interaction      29—30
Protein structure, tertiary structure, protein fold      29
Protein structure, tertiary structure, side chains      28
Protein structure, validation software and resources      215—216
Protein surrogates, structure-based drug design (SBDD)      490
Protein-ligand interactions, protein function identification      391—392
Protein-ligand interactions, ReliBase data source      224
Protein-nucleic acid complexes, Nucleic Acid Database (NDB) data      208—210
Protein-protein interaction, data resources      215 217
Protein-protein interaction, docking and ligand site characterization      445—446
Protein-protein interaction, electrostatic interactions      427—428
Protein-protein interaction, evolutionary prediction methods, coevolution      411
Protein-protein interaction, evolutionary prediction methods, conservation of positions      410
Protein-protein interaction, evolutionary prediction methods, family-dependent conservation      411
Protein-protein interaction, evolutionary prediction methods, future applications      421—422
Protein-protein interaction, evolutionary prediction methods, interaction partners      416—421
Protein-protein interaction, evolutionary prediction methods, interaction partners, genomic-based computation      417—418
Protein-protein interaction, evolutionary prediction methods, interaction partners, high-throughput applications      416
Protein-protein interaction, evolutionary prediction methods, interaction partners, protein databases and collections      416—417
Protein-protein interaction, evolutionary prediction methods, interaction partners, sequence-based computation      418—421
Protein-protein interaction, evolutionary prediction methods, interaction regions      411—416
Protein-protein interaction, evolutionary prediction methods, interaction regions, hybrid methods      413—416
Protein-protein interaction, evolutionary prediction methods, interaction regions, sequence-based methods      413
Protein-protein interaction, evolutionary prediction methods, interaction regions, structure-based methods      411—412
Protein-protein interaction, evolutionary prediction methods, research background      409—410
Protein-protein interaction, fold recognition, threading errors      535 537—539
Proton NMR ( $^{1}H$ NMR), macromolecular structure      90—91
Proton NMR ( $^{1}H$ NMR), macromolecular structure, bioinformatics      93—94
Proton NMR ( $^{1}H$ NMR), macromolecular structure, screening methods      94—96
PROVE software, error estimation and precision      296
Pseudorotation, sugar phosphate backbone conformation      49—55
PSI-BLAST algorithm, CATH domain structure database, sequence-based homologue protocols      253—255
PSI-BLAST algorithm, CATH domain structure database, superfamily relative recruitment      260
PSI-BLAST algorithm, fold recognition, divergent evolution      524
PSI-BLAST algorithm, fold recognition, protein families, multiple alignments      530—531
PSI-BLAST algorithm, fold recognition, protein sequence analysis      528—529
PSI-BLAST algorithm, one-dimensional secondary structure prediction      560—562
PSI-BLAST algorithm, one-dimensional secondary structure prediction, error detection      569—570
PSIPRED system, one-dimensional secondary structure prediction      561—562
PSIPRED system, one-dimensional secondary structure prediction, error rates      568—569
Puckering process, sugar phosphate backbone conformation      49—55
PUU algorithm, domain identification, assignment criteria      378—379
PUU algorithm, domain identification, CATH domain structure database      258
PUU algorithm, domain identification, second generation assignment algorithms      370—377
PyMol software, macromolecular visualization      144
Quality assurance, all-atom contacts, structure validation      303—304
Quality assurance, all-atom contacts, structure validation, current facilities and applications      311—317
Quality assurance, all-atom contacts, structure validation, protocols      305—307
Quality assurance, all-atom contacts, structure validation, vs. traditional criteria      308—311
Quality assurance, three-dimensional models, error estimation and precision      275—296
Quality assurance, three-dimensional models, error estimation and precision, deposited structures      284—296
Quality assurance, three-dimensional models, error estimation and precision, NMR spectroscopic errors      282—284
Quality assurance, three-dimensional models, error estimation and precision, x-ray crystallographic errors      275—282
Quality assurance, three-dimensional models, NMR spectroscopy models      273—274
Quality assurance, three-dimensional models, research background      271—272
Quality assurance, three-dimensional models, software      296
Quality assurance, three-dimensional models, web information sources      296—298
Quality assurance, three-dimensional models, x-ray crystallography models      272—273
QUANTA program, high-throughput crystallographic analysis, electron density map interpretation      80
Quantitative structure-activity relationships (QSAR), computer-aided drug design (CADD), analog-based design      444—445
Quantitative structure-activity relationships (QSAR), drug bioinformatics      477
Quantum force fields, homology model optimization      517—518
Quantum mechanics, ab initio fold prediction, potentials categories      548
Quantum mechanics, docking and ligand design      441—442
Quaternary protein structure, functional relevance      35—36
Quaternary protein structure, multiple polypeptide chains      33—36
Quaternary protein structure, Protein Quaternary Structure (PQS) database      222—223
Query/analysis capabilities, Nucleic Acid Database (NDB)      202—204
Query/analysis capabilities, Protein Data Bank (PDB)      191—193
QuickPDB, macromolecular visualization      145—148
R-factor      see also "Brunger's free R-factor"
R-factor, error estimation and precision, NMR models      283—284
R-factor, error estimation and precision, x-ray crystallography      280
Radial distribution function, homology modeling validation      519
Ramachandran Plot, peptide bond structure      19—20
Ramachandran Plot, protein structure, error estimation and precision      289—292
Ramachandran Plot, secondary protein structure      21
Ramachandran Plot, web-based visualization techniques      145—148
Random conical tilt, electron cryomicroscopy, single-particle analysis      122
Rank ordering, docking and ligand design, energies      463
Rapid Access Format (RAF), ASTRAL compendium      220—221
ras protein family, tree determinants      413
RasMol software, CATH domain structure database, Dictionary of Homologous Superfamilics (DHS)      259—260
RasMol software, CATH domain structure database, domain boundary identification      258
RasMol software, macromolecular visualization      138 141—142
RasMol software, web-based visualization techniques      146—148
Raster3D software, macromolecular visualization      143
Raw data management, protein structure, NMR spectroscopy      100—101

Real-space refinement algorithms, high-throughput crystallographic analysis, macromolecular structures      82
Reassembly issues, docking and ligand design      462—464
Reassembly issues, docking and ligand design, free energies of binding      463—464
Reassembly issues, docking and ligand design, geometric issues      462—463
Reassembly issues, docking and ligand design, ranker energy ordering      463
Reassembly issues, docking and ligand design, success/failure ratios      463
Receptor-ligand binding, docking and ligand design, combinatorial calculation      461
Receptor-ligand binding, docking and ligand design, database organization      466
Receptor-ligand binding, docking and ligand design, free energy      450—451
Reduce program, all-atom contact analysis      305—307
Reduce program, all-atom contact analysis, clashlistcluster script      313—316
Refinement techniques, all-atom contact analysis      309—311
Refinement techniques, high-throughput crystallographic analysis, macromolecular structure      81—82
Refinement techniques, protein structure, NMR spectroscopy      102
Refinement techniques, X-ray crystallography, three-dimensional models, uncertainty estimation      275—277
REFMAC program, high-throughput crystallographic analysis, macromolecular structures      82
ReliBase data source, protein-ligand interactions      224
REMARK records, Protein Data Bank (PDB) protocols      162—164
Remote Procedure Calling (RCP) protocol, Metalloprotein Database and Browser (MDB)      226
Research Col laboratory for Structural Bioinformatics (RCSB), Protein Data Bank (PDB), cooperation with      182
Research Col laboratory for Structural Bioinformatics (RCSB), Protein Data Bank (PDB), data deposition      187
Research Col laboratory for Structural Bioinformatics (RCSB), unavailable macromolecular structures      220
Residue exchange matrix, homology modeling, multiple sequence alignment      512—513
Residue exchange matrix, homology modeling, template identification and alignment      510—511
Residues, fold recognition, threading approximations      534—535
Residues, protein-protein interaction prediction, tree determinants      413
Residues, quaternary protein structure      34—36
Residues, tertiary protein structure, hydrophobic effect      29—30
Resolution parameters, X-ray crystallography, error estimation and precision      277—280
RESOLVE program, high-throughput crystallographic analysis, density modification      78
RESOLVE program, high-throughput crystallographic analysis, future applications      83—84
Restrained electrostatic potential (RESP), docking and ligand design, molecular mechanics scoring functions      458—459
Reverse transcriptase, web-based visualization      145—148
RFSRV method, fold recognition, algorithm comparison and assessment      539—540
Ribosome, Nucleic Acid Database (NDB), ribosomal subunit structures      210—211
Ribosome, structural characteristics      64—67
RiboWEB knowledge base, structural bioinformatics      9
Ribozymes, structural characteristics      63—64
Richards Box, macromolecular visualization      137
Rigid body structures, domain identification, first generation assignment algorithms      369—370
RIGOR database, protein function identification      399
RIKEN protocol, cell-free protein production      104—105
Ring pucker geometry, sugar phosphate backbone conformation      50—55
RNA, Nucleic Acid Database (NDB) information      200—201
RNA, Nucleic Acid Database (NDB) information, structural analysis      209—210
RNA, structural characteristics      41—42
RNA, structural characteristics, base pair geometry      45—49
RNA, structural characteristics, duplexes      60—62
RNA, structural characteristics, mismatches and bulges      62—63
RNA, structural characteristics, sugar phosphate backbone      49—55
RNAML syntax, Nucleic Acid Database (NDB) RNA structures      209—210
RNase P, ribozyme structure      63
Roll, base pair geometry      48
Roll, DNA duplexes      56—59
Root-mean-squared deviation, docking and ligand design, reassembly complexes      462—463
Root-mean-squared deviation, NMR structures, error estimates      283—284
Rosetta structure prediction, ab initio fold prediction, polypeptide chains      546—547
Rosetta structure prediction, ab initio fold prediction, structural genomics      551
Rotamer library, homology modeling, model optimization      516—518
Rotamer library, homology modeling, side-chain conformations      515—516
Rule-of-five quantitative assessment, drug bioinformatics, genomic druggability      481—483
Rule-of-five quantitative assessment, drug bioinformatics, target druggability      480—481
Saddle-point construction, Poisson — Boltzmann equation (PBE), electrostatic interactions      430
Salt bridge, tertiary protein structure      30
SAM-T99sec system, one-dimensional secondary structure prediction      561—562
Sampling techniques, docking and ligand design, combinatorial calculation      461
Sampling techniques, macromolecular structure, NMR spectroscopy      96—97
Sampling techniques, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study      597—599
SAMT profiles, CATH domain structure database, sequence-based homologue protocols      253—255
SAMT profiles, CATH domain structure database, superfamily relative recruitment      260
SARF2, comparison algorithm optimization      326
SARF2, protein structure representation      325
SARF2, statistical testing      326
Save frames, macromolecular Crystallographic Information File (mmCIF)      167—168
Scattering techniques, electron cryomicroscopy      116—119
Scientific method, bioinformatics and      3—4
Scoring functions, docking and ligand design, background      445
Scoring functions, docking and ligand design, empirical methods      457
Scoring functions, docking and ligand design, first principles methods      456
Scoring functions, docking and ligand design, future research      465—466
Scoring functions, docking and ligand design, knowledge-based potentials      457
Scoring functions, docking and ligand design, molecular mechanics      457—461
Scoring functions, docking and ligand design, molecular mechanics, charge representation      457—459
Scoring functions, docking and ligand design, molecular mechanics, solvent representation      459—461
Scoring functions, docking and ligand design, molecular mechanics, van der Waals radii      459
Scoring functions, docking and ligand design, semiempirical methods      456
Scoring functions, fold recognition, protein sequence analysis      527—529
Scoring functions, fold recognition, threading approximations      534—535
Scoring functions, homology modeling, multiple sequence alignment      512—513
Screening techniques, macromolecular structure, NMR spectroscopy      94—96
Search space, structural bioinformatics      6—7
Search techniques, ab initio fold prediction      548—549
SearchFields interlace, Protein Data Bank (PDB), user web access      191—193
SearchLite interface, Protein Data Bank (PDB), user web access      191—193
Second generation assignment algorithms, domain identification      370—377
Secondary protein structure, $\alpha$ -helices      22—24
Secondary protein structure, $\beta$ sheets      24
Secondary protein structure, data sources      215—216 218
Secondary protein structure, data sources, ASTRAL compendium, sequence and structure relationships      220—221
Secondary protein structure, data sources, Derived Secondary Structure of Proteins (DSSP)      222
Secondary protein structure, data sources, HIV Proteases resource (HIVpr)      225
Secondary protein structure, data sources, MacroMolecular DataBase (MMDB)      221—222
Secondary protein structure, data sources, Macromolecular Motions Database (MolMovDB)      226—227
Secondary protein structure, data sources, Metalloprotein Database and Browser (MDB)      225—226
Secondary protein structure, data sources, PartsList dynamic fold comparisons      227—228
Secondary protein structure, data sources, Protein Kinase Resource (PKR)      224—225
Secondary protein structure, data sources, Protein Quaternary Structure (PQS)      222—223
Secondary protein structure, data sources, ReliBase, protein-ligand interaction      224
Secondary protein structure, data sources, Swiss-Model automated comparative modeling      228
Secondary protein structure, data sources, targets and prediction methods      228—229
Secondary protein structure, evolutionary mechanisms      239
Secondary protein structure, fold recognition      524
Secondary protein structure, local three-dimensional model      20—28
Secondary protein structure, loops and coils      24—28
Secondary protein structure, one-dimensional models, emerging and future technologies      571—574
Secondary protein structure, one-dimensional models, evaluation of prediction techniques      566—568
Secondary protein structure, one-dimensional models, practical applications      568—571
Secondary protein structure, one-dimensional models, prediction techniques      558—562
Secondary protein structure, one-dimensional models, programs and public servers      566
Secondary protein structure, one-dimensional models, solvent accessibility prediction      562—563
Secondary protein structure, one-dimensional models, theoretical background      557—558
Secondary protein structure, one-dimensional models, transmembrane helix prediction      563—566
Secondary protein structure, structure assignment, assignment techniques      344—346
Secondary protein structure, structure assignment, assignment techniques, DEFINE algorithm      345
Secondary protein structure, structure assignment, assignment techniques, DSSP      344
Secondary protein structure, structure assignment, assignment techniques, DSSPcont      346 353—356
Secondary protein structure, structure assignment, assignment techniques, P-curve      345—346
Secondary protein structure, structure assignment, assignment techniques, STRIDE      344—345
Secondary protein structure, structure assignment, automatic comparisons      347—349
Secondary protein structure, structure assignment, empirical calculation      343
Secondary protein structure, structure assignment, future research issues      351—356
Secondary protein structure, structure assignment, hydrogen bond models      341—343
Secondary protein structure, structure assignment, hydrogen bond models, angle-distance assignment      341—342
Secondary protein structure, structure assignment, hydrogen bond models, Coulomb calculation      342—343
Secondary protein structure, structure assignment, NMR structures      351
Secondary protein structure, structure assignment, programs and databases      346—347
Secondary protein structure, structure assignment, research background      339—341
Secondary protein structure, structure assignment, sequence distributions      351
Secondary protein structure, structure assignment, STICK geometric-based continuous assignment      353
Secondary protein structure, structure assignment, supersecondary structures      351—353
Secondary protein structure, structure assignment, three classes conversions      349—351
Secondary structure elements (SSEs), comparison algorithm optimization, SARF2      326
Secondary structure elements (SSEs), protein structure comparison and alignment, DALI database      324
Secondary structure elements (SSEs), protein structure comparison and alignment, SARF2      325
Segmentation algorithms, electron cryomicroscopy, pattern recognition      128
Selectivity criteria, drug bioinformatics, target triage      485—486
Self-cleaving RNA, ribozyme structure      63
Self-defining Texty Archive and Retrieval (STAR), macromolecular Crystallographic Information File (mmCIF)      165—169
Self-parameterizing force fields, homology modeling optimization      517—518
Self-threading energy, fold recognition, threading errors      535 537—539

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