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

Three-dimensional models, homology modeling, side-chain modeling      514—516
Three-dimensional models, homology modeling, template recognition and initial alignment      510—511
Three-dimensional models, homology modeling, validation procedures      518—519
Three-dimensional models, limitations      557—558
Three-dimensional models, one-dimensional secondary structure prediction, evolution to      572
Three-dimensional models, protein function identification      391—392
Three-dimensional models, quality assurance, error estimation and precision      275—296
Three-dimensional models, quality assurance, error estimation and precision, deposited structures      284—296
Three-dimensional models, quality assurance, NMR spectroscopic errors      282—284
Three-dimensional models, quality assurance, NMR spectroscopy models      273—274
Three-dimensional models, quality assurance, research background      271—272
Three-dimensional models, quality assurance, software      296
Three-dimensional models, quality assurance, web information sources      296—298
Three-dimensional models, quality assurance, x-ray crystallographic errors      275—282
Three-dimensional models, quality assurance, x-ray crystallography models      272—273
Three-dimensional models, secondary protein structure      20—28
Three-dimensional models, secondary protein structure, $\alpha$ -helices      22—24
Three-dimensional models, secondary protein structure, $\beta$ sheets      24
Three-dimensional models, secondary protein structure, loops and coils      24—28
Three-dimensional models, structure comparison and alignment, algorithms and optimization      325—326
Three-dimensional models, structure comparison and alignment, defined      319—320
Three-dimensional models, structure comparison and alignment, evaluation of      327—328
Three-dimensional models, structure comparison and alignment, future applications      332—333
Three-dimensional models, structure comparison and alignment, multiple structure alignment      329—330
Three-dimensional models, structure comparison and alignment, protein fold space mapping      330—332
Three-dimensional models, structure comparison and alignment, protein structures      324—325
Three-dimensional models, structure comparison and alignment, protocols and methods      322—327
Three-dimensional models, structure comparison and alignment, sample results      328—329
Three-dimensional models, structure comparison and alignment, statistical analysis of results      326—327
Three-dimensional models, structure comparison and alignment, three-dimensional applications      320—321
Three-dimensional models, visualization software      141—144
Three-dimensional structures, structural bioinformatics      5
Tilt, base pair geometry      48
TMAP program, one-dimensional secondary structure prediction, transmembrane helix prediction      565—566
TMHMM program, one-dimensional secondary structure prediction, transmembrane helix prediction      566
Tool kits, macromolecular visualization      148—149
Topology fingerprint threading algorithm, fold recognition      538—539
TopPred2 system, one-dimensional secondary structure prediction, transmembrane helix prediction      565—566
Torsion angle dynamics (TAD) program, protein structure, NOE assignment and structure calculation      101—102
Torsion angles, all-atom contact analysis      310—311
Torsion angles, error estimation and precision, side chain models      292
Torsion angles, sugar phosphate backbone conformation      54—55
Trans values, sugar phosphate backbone conformation      55
Transfer RNA (tRNA), Nucleic Acid Database (NDB) information      200—201
Transfer RNA (tRNA), ribosome structure      64—67
Transfer RNA (tRNA), structural characteristics      61 63
Translation-Liberation-Screw (TLS) parameters, high-throughput crystallographic analysis, macromolecular structures      83
Transmembrane helix prediction, one-dimensional secondary structure prediction, basic concepts      563—566
Transmembrane helix prediction, one-dimensional secondary structure prediction, evaluation of      570—571
Transmembrane helix prediction, one-dimensional secondary structure prediction, evaluation of programs      566—567
Tree determinants, family-dependent conservation      411
Tree determinants, protein-protein interaction prediction      413
Triage research, drug bioinformatics, target triage      483—486
Triose phosphate isomerase (TIM) barrel structure, domain identification, first generation assignment algorithms      367—370
Triose phosphate isomerase (TIM) barrel structure, domain identification, second generation assignment algorithm      375—377
Triose phosphate isomerase (TIM) barrel structure, domain identification, splitting procedures      377
Triose phosphate isomerase (TIM) barrel structure, fold recognition      523—525
Triose phosphate isomerase (TIM) barrel structure, protein function identification      393—394
TROSY methodology, macromolecular structure, protein structural analysis      98
Tsukuba Accord, base pair geometry      48
Tsukuba Accord, Nucleic Acid Database (NDB) information      201
Tubulin, electron cryomicroscopy, three-dimensional crystalline arrays      121
TurboFrodo, high-throughput crystallographic analysis, electron density map interpretation      80
Two-dimensional models, Cambridge Structural Database (CSD) sources      219
Two-dimensional models, electron cryomicroscopy, research background      115—116
Two-dimensional models, electron cryomicroscopy, three-dimensional reconstruction      119—125
Two-dimensional models, one-dimensional secondary structure prediction, evolution to      572
Two-dimensional models, protein structure comparison and alignment, DALI database      324
Two-level dynamic programming, fold recognition, threading approximations      534—535
Uncertainty estimation, X-ray crystallography, three-dimensional models      275—277
Uniformity protocols, Protein Data Bank (PDB) data      187—189
User interface, SCOP organization and capabilities      244—246
User web access Protein Data Bank (PDB)      191—193
Validation procedures, all-atom contacts      303—304
Validation procedures, all-atom contacts, current facilities and applications      311—317
Validation procedures, all-atom contacts, drug bioinformatics, traget validation      486—487
Validation procedures, all-atom contacts, high-throughput crystallographic analysis, macromolecular structures      82
Validation procedures, all-atom contacts, homology modeling      518—519
Validation procedures, all-atom contacts, macromolecular structures, NMR spectroscopy      102—103
Validation procedures, all-atom contacts, Nucleic Acid Database (NDB) information      201—202
Validation procedures, all-atom contacts, Protein Data Bank (PDB) data acquisition      184—186
Validation procedures, all-atom contacts, protocols      305—307
Validation procedures, all-atom contacts, vs. traditional criteria      308—311
Validation procedures, all-atom contacts, website information      298
Van der Waals contacts, ab initio fold prediction, potentials categories      548
Van der Waals contacts, all-atom contact analysis      305—307
Van der Waals contacts, docking and ligand design, complex formation      450—454
Van der Waals contacts, docking and ligand design, molecular mechanics scoring functions      459
Van der Waals contacts, homology modeling, side-chain conformations      516

Van der Waals contacts, homology modeling, validation procedures      518—519
Vector Alignment Search Tool (VAST), comparison algorithm optimization      326
Vector Alignment Search Tool (VAST), MacroMolecular Database (MMDB)      222
Vector Alignment Search Tool (VAST), protein structure comparison and alignment      325
Vector Alignment Search Tool (VAST), statistical testing      327
Vector graphics systems, macromolecular visualization      137—138
Virtual library, docking and ligand design      449—450
Virtual screening, docking and ligand design      464
Virtual screening, drug bioinformatics, chemical lead identification      488
Visualization techniques, macromolecular structure, historical background      135—144
Visualization techniques, macromolecular structure, software summary table      150—156
Visualization techniques, macromolecular structure, toolkits      148—149
Visualization techniques, macromolecular structure, web-based software      145—148
Visualization techniques, structural bioinformatics      7
Visualization techniques, structural bioinformatics, image creation      10
Web-based visualization, macromolecular structures      145—148
WebMol, macromolecular visualization      145—148
Website addresses, all-atom contact analysis      316—317
Website addresses, ASTRAL compendium      220—221
Website addresses, Biological Macromolecule Crystallization Database (BMCD)      218—219
Website addresses, CATH domain structure database      261—263
Website addresses, Derived Secondary Structure of Proteins (DSSP)      222
Website addresses, HIV Proteases resource (HIVpr)      225
Website addresses, interacting protein databases      416—417
Website addresses, MacroMolecular DataBase (MMDB)      221
Website addresses, Macromolecular Motions Database (MolMovDB)      226—227
Website addresses, Metalloprotein Database and Browser (MDB)      225—226
Website addresses, Nucleic Acid Database (NDB)      204—206
Website addresses, one-dimensional secondary structure prediction      566—567
Website addresses, PartsList database      227—228
Website addresses, PDBsum website summaries      296—297
Website addresses, Protein Data Bank (PDB), application web access      193—194
Website addresses, Protein Data Bank (PDB), outreach sites      194—195
Website addresses, Protein Data Bank (PDB), user web access      191—193
Website addresses, Protein Kinase Resource (PKR)      224—225
Website addresses, Protein Quaternary Structure (PQS) resource      222—223
Website addresses, protein structure      36
Website addresses, ReliBase data source      224
Website addresses, Research Collaboratory for Structural Bioinformatics (RCSB), unavailable macromolecular structures      220
Website addresses, secondary protein structure, assignment protocols      346—347
Website addresses, structure comparison and alignment      323
Website addresses, Swiss-Model database      228
WHAT IF program, error estimation and precision      296
WHAT IF program, error estimation and precision, atom-atom contacts      294
WHAT IF program, structural studies, validation      102—103
WHATCHECK program, ASTRAL compendium      221
WHATCHECK program, error estimation and precision      296
WHATCHECK program, PDBREPORT results      298
WHATCHECK program, PDBsum website summaries      297
Wrong amino acid partners-correct interactions approximation, fold recognition, threading errors      537—539
Wrong amino acid partners-wrong interactions approximation, fold recognition, threading errors      538—539
Wrong partners-correct interactions (WC) approximation, fold recognition, threading errors      535 537—539
Wrong partners-wrong interactions (WW) approximation, fold recognition, threading errors      537—539
X and Y displacements, base pair geometry      47—48
X-ray crystallography, electron cryomicroscopy and      125—127
X-ray crystallography, error estimation and precision, three-dimensional models      275—282
X-ray crystallography, error estimation and precision, three-dimensional models, atomic B-factors      281
X-ray crystallography, error estimation and precision, three-dimensional models, average positional error      281
X-ray crystallography, error estimation and precision, three-dimensional models, Bruenger's free R-factor      280—281
X-ray crystallography, error estimation and precision, three-dimensional models, global parameters      277—281
X-ray crystallography, error estimation and precision, three-dimensional models, R-factor      280
X-ray crystallography, error estimation and precision, three-dimensional models, resolution      277—280
X-ray crystallography, error estimation and precision, three-dimensional models, selection criteria      281—282
X-ray crystallography, error estimation and precision, three-dimensional models, uncertainty estimation      275—277
X-ray crystallography, macromolecular structure, vs. nuclear magnetic resonance (NMR) spectroscopy      90
X-ray crystallography, modeling techniques, quality assurance      272—273
X-ray crystallography, Protein Data Bank (PDB) data content      184—186
X-ray crystallography, structural bioinformatics      8
X-ray crystallography, structural genomics, yeast mevalonate-5-diphosphate decarboxylase (MDD) case study      599
XEASY program, protein structure, NMR spectroscopy      100—102
XEASY program, protein structure, NOE assignment and structure calculation      101—102
XFit, macromolecular visualization      141
XML      see "Extensible markup language (XML)"
YcaC gene product, protein function identification      401—402
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics      597—604
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, biomedical implications      604
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, evolutionary mechanisms      601
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, homology modeling      600—601
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, homology modeling, MDD/HSK structures      601
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, progress summary      604—605
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, sample preparation and characterization      597—599
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, structural overview      599—600
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, target selection      597 601—604
Yeast mevalonate-5-diphosphate decarboxylase (MDD), structural genomics, x-ray structure determination      599
Yeast two hybrid techniques, protein-protein interaction prediction      421—422
Z-DNA, conformation      56 58—59
Z-DNA, Nucleic Acid Database (NDB) data      206—210
Z-DNA, structural analysis      42
Zinc-finger motif, secondary structure assignment      351—353
Zinc-finger motif, tertiary protein structure      30

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