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

Главная Ex Libris Книги Журналы Статьи Серии Каталог Wanted Загрузка ХудЛит Справка Поиск по индексам Поиск Форум

Авторизация

Поиск по указателям

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

Обсудите книгу на научном форуме

Нашли опечатку?
Выделите ее мышкой и нажмите Ctrl+Enter

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

"Frozen approximation", fold recognition, threading algorithms      534—535
"Frozen approximation", fold recognition, threading errors      538—539
"Kissing-loop" structure, mismatched/bulged RNA      62—63
"Knobs-into-holes" geometry, one-dimensional secondary structure prediction      561—562
"Thawing" approximation, fold recognition, threading errors      538—539
"Training set" proteins, structural bioinformatics      6
"Twilight zone" sequencing, fold recognition, protein sequence analysis      528—529
"Twilight zone" sequencing, one-dimensional secondary structure prediction      559—562
$\alpha$ -helices, high-throughput crystallographic analysis, electron density map interpretation      80
$\alpha$ -helices, SCOP hierarchical classification      240-241
$\alpha$ -helices, secondary protein structure, assignment protocols, DEFINE algorithm      345
$\alpha$ -helices, secondary protein structure, assignment protocols, Dictionary of Secondary Structure of Proteins (DSSP) techniques      344
$\alpha$ -helices, secondary protein structure, assignment protocols, P-Curve assignment scheme      345—346
$\alpha$ -helices, secondary protein structure, assignment protocols, STRIDE protocol      344—345
$\alpha$ -helices, secondary protein structure, properties      22—24
$\alpha$ -helices, secondary protein structure, three-dimensional models      21
$\beta$ sheets, high-throughput crystallographic analysis, electron density map interpretation      80
$\beta$ sheets, SCOP hierarchical classification      240—241
$\beta$ sheets, secondary protein structure, assignment protocols      345—346
$\beta$ sheets, secondary protein structure, assignment protocols, DEFINE algorithm      345
$\beta$ sheets, secondary protein structure, assignment protocols, Dictionary of Secondary Structure of Proteins (DSSP) techniques      344
$\beta$ sheets, secondary protein structure, assignment protocols, STRIDE protocol      344—345
$\beta$ sheets, secondary protein structure, properties      24
$\beta$ sheets, secondary protein structure, three-dimensional models      21
$\gamma$ perturbation method, high-throughput crystallographic analysis, density modification      78
2,2-Dimethylsilapentane-5-sulfonic acid (DSS), macromolecular structure, NMR spectroscopy      93—94
5S RNA, all-atom contacts      313—316
A-DNA, base pair geometry      47—49
A-DNA, Nucleic Acid Database (NDB) data      206—210
A-DNA, pucker structures      56 58—59
A-RNA, duplex structure      60-62
A-RNA, hammerhead ribozymes      61 64
A-RNA, mismatched/bulged RNA      62—63
A-RNA, transfer RNA (tRNA) structure      61 63
Ab initio fold prediction, applications      549—551
Ab initio fold prediction, applications, genome annotation      549—550
Ab initio fold prediction, applications, structural genomics      550-551
Ab initio fold prediction, Critical Assessment for Structure Prediction (CASP), comparative modeling      502—503
Ab initio fold prediction, Critical Assessment for Structure Prediction (CASP), fold recognition      503
Ab initio fold prediction, Critical Assessment for Structure Prediction (CASP), novel fold recognition      503—504
Ab initio fold prediction, Critical Assessment for Structure Prediction (CASP), research background      499—501
Ab initio fold prediction, Critical Assessment for Structure Prediction (CASP), summary of progress      501—502
Ab initio fold prediction, docking and ligand design, molecular mechanics scoring functions, charge representation      457—459
Ab initio fold prediction, future research      551—552
Ab initio fold prediction, homology modeling      510
Ab initio fold prediction, homology modeling, loop regions      514
Ab initio fold prediction, physics principles and      531 533
Ab initio fold prediction, polypeptide chain representations      546—547
Ab initio fold prediction, potentials categories      547—548
Ab initio fold prediction, protein function identification      396—397
Ab initio fold prediction, search methods      548—549
Ab initio fold prediction, structural assignment, Coulomb hydrogen bond calculation      343
Ab initio fold prediction, structural bioinformatics      8
Ab initio fold prediction, structural bioinformatics, prediction techniques      10
Ab initio fold prediction, theoretical background      545
Access issues, Nucleic Acid Database (NDB)      203—204
Access issues, Nucleic Acid Database (NDB), mirror sites      205—206
Access issues, one-dimensional secondary structure prediction      572
Access issues, Protein Data Bank (PDB)      189—194
Access issues, Protein Data Bank (PDB), application web access      193—194
Access issues, Protein Data Bank (PDB), database architecture      190-191
Access issues, Protein Data Bank (PDB), ftp access      194
Access issues, Protein Data Bank (PDB), user web access      191—193
Access issues, quality assurance information      296—298
Accessible surface area (ASA), docking and ligand orientation      453—454
Actin filaments, electron cryomicroscopy, protein dynamics      124—125
Actin filaments, electron cryomicroscopy, three-dimensional reconstruction      121
Active sites, secondary protein structure      24—28
Adaptive finite element discretization, electrostatic interactions, Poisson — Boltzmann equation (PBE)      433—435
ADME (absorption, distribution, metabolism, and excretion) modeling, docking and ligand design      468
ADME (absorption, distribution, metabolism, and excretion) modeling, drug modeling      490
ADMET (absorption, distribution, metabolism, excretion, and toxicology) modeling, drug bioinformatics, pharmaceutical models      479
Algorithm development, structural bioinformatics      4—6
Algorithm development, structural bioinformatics, structural assessment and evaluation      9
Aligned fragment pair (AFP), protein structure representation, combinatorial extension (CE) algorithm      324
Aligned fragment pair (AFP), structure comparison and alignment, CE algorithm optimization      325
Alignment      see "Structure comparison and alignment"
Alignment algorithms, fold recognition, threading approximation      534—535
Alignment algorithms, homology modeling, template identification and alignment      510-511
Alp molecular switch, protein function identification, Mjo577 genome      400—401
Alpha/beta hydrolase fold, protein function identification      393—394
AM1—BCC model, docking and ligand design, molecular mechanics scoring functions      458—459
AMBER force fields, docking and ligand design, free energy binding      464
AMBER force fields, docking and ligand design, molecular mechanics scoring functions      458—459
AMBER force fields, nucleic acid chemical structure      42—45
Amino acid sequence, domain identification      380
Amino acid sequence, fold recognition, threading errors      537—539
Amino acid sequence, homology modeling      507—510
Amino acid sequence, one-dimensional secondary structure, prediction, theoretical background      558—562
Amino acid sequence, protein structure      16—20
Amino acid sequence, protein structure, amino acid structures      16—17
Amino acid sequence, protein structure, peptide bond      17—20
Analogue structures, computer-aided drug design (CADD)      444—445
Analogue structures, protein function identification      395—396
Angle-distance hydrogen bond assignment, secondary protein structures      341—342
Angular reconstitution, electron cryomicroscopy, single-particle analysis      122
Annotation of data, Protein Data Bank (PDB) information      184—186
ANOLEA program, error estimation and precision, atom-atom contacts      294
Anomalous diffraction, high-throughput, crystallographic analysis, macromolecular structures      77
Anti conformation, A-DNA      56 58—59
Anti conformation, sugar phosphate backbone conformation      53—55
Anti conformation, Z-DNA      59
Antiparallel structures, $\beta$ -sheets, secondary protein structure      24
Application program interface (API), format and protocols      178
Application program interface (API), Protein Data Bank (PDB) architecture, application web access      193—194
Application web access, Protein Data Bank (PDB)      193—194
AQUA program, protein structure, validation      102—103
Aquaporin, electron cryomicroscopy, three-dimensional crystalline arrays      121
Asn/Gln flips, all-atom contact analysis      311—316
Assay design, drug bioinformatics, lead identification      487
Assembly mechanisms, quaternary protein structure      35
ASTRAL compendium, sequence and structure relationships data      220-221
Atom-atom contacts, domain identification      365—367
Atom-atom contacts, error estimation and precision      292—294
Atom-atom contacts, homology modeling validation      519
Atom-atom contacts, structure validation      303—304
Atom-atom contacts, structure validation, current facilities and applications      311—317
Atom-atom contacts, structure validation, protocols      305—307
Atom-atom contacts, structure validation, vs. traditional criteria      308—311
ATOM/HETATM data, ASTRAL, compendium secondary data      220—221
Atomic nomenclature, Protein Data Bank (PDB) data validation and annotation      186
Atomic positions, homology model optimization      516—518
Atomic positions, macromolecular Crystallographic Information File (mmCIF)      173—175
Atomic solvation parameters (ASP), docking and ligand design, solvent representation      460—461
Atoms in molecules (AIM) theory, docking and ligand design, molecular mechanics scoring functions      458—459
ATPases, drug bioinformatics, target druggability      479—480
AutoDep Input Tool (ADIT), Nucleic Acid Database (NDB) validation      201—202
AutoDep Input Tool (ADIT), nucleic acid structures, error estimation and precision      294—295
AutoDep Input Tool (ADIT), Protein Data Bank (PDB), data acquisition and deposition      182 187
AUTODOCK software, ligand orientation      447—448
Automation techniques, comparative modeling sources, Swiss-Model database      228
Automation techniques, high-throughput crystallographic analysis, disorder      83
Automation techniques, high-throughput crystallographic analysis, noncrystallographic symmetry      82—83
Automation techniques, high-throughput crystallographic analysis, research background      76
Automation techniques, secondary protein structure, assignment comparisons      347—349
Automation techniques, secondary protein structure, structure assignment      340—341
Average positional error, x-ray, crystallography models      281
AVS software, macromolecular visualization      144
B-DNA, base pair geometry      47—49
B-DNA, duplexes      55—59
B-DNA, Nucleic Acid Database (NDB) data      206—210
B-DNA, structural analysis      42
B-factors models, all-atom contact analysis      308—311
B-factors models, quality assurance      272—273
B-factors models, x-ray crystallography models, atomic B-factor errors      281
B-factors models, x-ray crystallography models, uncertainty estimation      275—277
Back-calculation techniques, error estimation and precision, NMR models      283—284
Backbone conformation, ab initio fold prediction, polypeptide chains      546—547
Backbone conformation, all-atom contact analysis      310—316
Backbone conformation, homology modeling      508—510 513

Backbone conformation, homology modeling, loop regions      513—514
Backbone conformation, homology modeling, side-chain conformations      515—516
Bacterial hydrolase, protein function identification      401—402
Ball-and-stick model, $\alpha$ -helices      22—24
Ball-and-stick model, electrostatic interactions, Poisson — Boltzmann equation (PBE)      430—432
Base pairing, DNA duplexes      55—59
Base pairing, geometry      45—49
Base pairing, geometry, buckle      46—47
Base pairing, geometry, helical twist      49
Base pairing, geometry, inclination      47
Base pairing, geometry, propeller twist      46—47
Base pairing, geometry, roll      49
Base pairing, geometry, tilt      49
Base pairing, geometry, X and Y displacements      47—48
Base pairing, nucleic acid chemical structure      42—45
Base pairing, Nucleic Acid Database (NDB) data      208—210
Base pairing, sugar phosphate backbone conformation      50—55
Bidirectional recurrent neural networks (BRNN) complex, one-dimensional secondary structure prediction      561—562
Bifunctional proteins, IMPase structure      402
BIND database, protein-protein interaction prediction      417
Binding sites, docking and ligand design, complex formation      450—454
Binding sites, docking and ligand design, free energies      463—464
Binding sites, docking molecules      445
Binding sites, drug bioinformatics, target druggability      479—481
Binding sites, fold recognition, convergent evolution      524
Bioinformatics      see also "Structural bioinformatics"
Bioinformatics, defined      3—7
Bioinformatics, SCOP organization and capabilities      244—246
Biological Macromolecule Crystallization Database (BMCD), primary data sources      218—219
Biological Macromolecule Crystallization Database (BMCD), Protein Data Bank (PDB) architecture      191
Biology-based fold recognition, molecular evolution, sequence similarity and homology      527
Biology-based fold recognition, protein families and multiple alignments      529—531
Biology-based fold recognition, protein sequence analysis      527—529
Biology-based fold recognition, theoretical background      526
BioMagResBank (BMRB), macromolecular structure, NMR spectroscopy      91—94
BioMagResBank (BMRB), macromolecular structure, validation      103
Biopolymers, electrostatic interactions      426
BioSync dictionary, format and content      175
Birdwash toolkit, macromolecular visualization      149
BLAST search techniques, fold recognition, protein sequence analysis      528—529
BLAST search techniques, homology modeling, template identification and alignment      510—511
BLAST search techniques, MacroMolecular Database (MMDB)      221—222
BLAST search techniques, SCOP organization and capabilities      242—244
BLAST search techniques, Swiss-Model database      228
Blue Gene computer, homology model optimization      518
Bobscript, macromolecular visualization      143
Boltzmann constant, docking and ligand design      452—454
Boltzmann constant, electrostatic interactions, Poisson equation      429—430
Bond distances, all-atom contact analysis      310—311
Born ion model, electrostatic interactions      427
Boundary identification, CATH domain structure database      258
Brownian dynamics, electrostatic interactions      427
Brunger's free R-tactor, x-ray crystallography, error estimation and precision      280—281
Buckle sign, base pair geometry      46—47
Bulged RNA, structural characteristics      62—63
C-alpha only structures, domain identification      364—365
C-alpha only structures, domain identification, amino acid sequence      380
C-alpha only structures, error estimation and precision      294
C2 domains, electrostatic interactions      427—428
Calcium complex, macromolecular structure, NMR spectroscopy      95—96
Cambridge Accord conventions, base pair geometry      45—49
Cambridge Crystallographic Data Center (CCDC)      219—220
Cambridge Structural Database (CSD), high-throughput crystallographic analysis      76
Cambridge Structural Database (CSD), macromolecular structure, validation      102—103
Cambridge Structural Database (CSD), primary information sources      219—220
Capsid structures, electron cryomicroscopy, single-particle analysis      122
Carbohydrate modification, tertiary protein structure      30
Carbon-13 nuclei, macromolecular structure, NMR spectroscopy      90—91
Carboxyl group (COOH), amino acid sequence      16—17
Cartesian meshes, electrostatic interactions, Poisson — Boltzmann equation (PBE)      432—433
CATH (Class, Architecture, Topology, and Homology) domain structure database, boundary identification      258
CATH (Class, Architecture, Topology, and Homology) domain structure database, comparison with SCOP and DALI      247—248
CATH (Class, Architecture, Topology, and Homology) domain structure database, domain identification, assignment criteria      377—379
CATH (Class, Architecture, Topology, and Homology) domain structure database, domain identification, second generation assignment algorithms      374—377
CATH (Class, Architecture, Topology, and Homology) domain structure database, fold recognition, limitations      524—525
CATH (Class, Architecture, Topology, and Homology) domain structure database, GENE3D resource      260—261
CATH (Class, Architecture, Topology, and Homology) domain structure database, historical development      248—252
CATH (Class, Architecture, Topology, and Homology) domain structure database, homologous structures, sequence-based protocols      253—255
CATH (Class, Architecture, Topology, and Homology) domain structure database, homologous structures, structure-based methods      255—257
CATH (Class, Architecture, Topology, and Homology) domain structure database, homologous structures, superfamily dictionaries      259—260
CATH (Class, Architecture, Topology, and Homology) domain structure database, homologous structures, superfamily sequence relatives      260
CATH (Class, Architecture, Topology, and Homology) domain structure database, multiple structure alignments, 3D templates      257
CATH (Class, Architecture, Topology, and Homology) domain structure database, population statistics, folds in architectures      263—264
CATH (Class, Architecture, Topology, and Homology) domain structure database, population statistics, superfamily/family folds      264—267
CATH (Class, Architecture, Topology, and Homology) domain structure database, protein fold space mapping      330—332
CATH (Class, Architecture, Topology, and Homology) domain structure database, protein function identification      397
CATH (Class, Architecture, Topology, and Homology) domain structure database, server applications      263—267
CATH (Class, Architecture, Topology, and Homology) domain structure database, structural/phylogenctic identification      249—260
CATH (Class, Architecture, Topology, and Homology) domain structure database, update protocols      262—263
CATH (Class, Architecture, Topology, and Homology) domain structure database, web site and server protocols      261—263
CE database, Protein Data Bank (PDB) architecture      191
Cell-free protein production, NMR spectroscopy      104—105
Cellular genomes, amino acid sequence      17
Cellular genomes, electrostatic interactions, Poisson — Boltzmann equation (PBE)      435—436
Change-coupled device (CCD), electron cryomicroscopy, electron tomography      123
Change-coupled device (CCD), electron cryomicroscopy, optics and image formation      116—119
Charge representation, docking and ligand design, molecular mechanics scoring functions      457—459
Charged amino acids, side chain sequence      17
CHARMM force fields, nucleic acid chemical structure      42—45
Chemical leads, drug bioinformatics, identification      487—488
Chemical leads, drug bioinformatics, optimization      489—490
Chemical libraries, drug bioinformatics      488
Chemical shift protocols, macromolecular structure, concerted techniques      106
Chemical shift protocols, macromolecular structure, NMR spectroscopy      92—94
Chemical shift protocols, macromolecular structure, validation      103
Chemical shift protocols, protein structure, NMR spectroscopy      100—102
Chime browser, web-based visualization techniques      146—148
Chimera software, macromolecular visualization      143—144
Clash score, all-atom contact analysis      308—311
Clash score, all-atom contact analysis, PDB files      311—316
Clashlistcluster script, all-atom contacts      313—316
Classification protocols, structural bioinformatics      10
CLIX, docking and ligand site characterization      445—446
Close contacts, Protein Data Bank (PDB) data validation and annotation      186
CLUSTALW program, homology modeling, multiple sequence alignment      512—513
CLUSTALW program, told recognition, protein sequence analysis      528—529
CNS program, protein structure, validation      103
Co-localization, quaternary protein structure      35
Coevolution, protein-protein interaction prediction      411
Coil regions, secondary protein structure      24—28
Coiled-coil predictions, one-dimensional secondary structure prediction      561—562
COILS program, one-dimensional secondary structure prediction      561—562
Combinatorial brand-and-bound minimization algorithm, fold recognition, ahreading approximations      534—535
Combinatorial calculation, docking and ligand design, receptor flexibility      461
Combinatorial calculation, docking and ligand design, sampling issues      461
Combinatorial extension (CE) algorithm, multiple structure alignments      329—330
Combinatorial extension (CE) algorithm, protein fold space mapping      330—332
Combinatorial extension (CE) algorithm, protein kinase alignments      327—328
Combinatorial extension (CE) algorithm, statistical testing      326
Combinatorial extension (CE) algorithm, structure comparison and alignment      323—327
Combinatorial extension (CE) algorithm, structure comparison and alignment, optimization      325
Combinatorial extension (CE) algorithm, structure comparison and alignment, protein structure representation      324
Combinatorial subunits, quaternary protein structure      35
Common Gateway Interface (CGI), Protein Data Bank (PDB) architecture      191
Common Gateway Interface (CGI), Protein Data Bank (PDB) architecture, application web access      193—194
Common Object Request Broker Architecture (CORBA), database interoperability      231
Common Object Request Broker Architecture (CORBA), format and protocols      178
Common Object Request Broker Architecture (CORBA), Protein Data Bank (PDB), future applications      196
Comparative modeling, Critical Assessment for Structure Prediction (CASP), procedures      502—503
Comparative modeling, Critical Assessment for Structure Prediction (CASP), research background      499—501
COMPARER system, comparison algorithm optimization      325—326
COMPARER system, protein structure representation      325
COMPARER system, statistical testing      326
Comparison algorithms, structure comparison arid alignment      325—326
Complex reassembly, docking and ligand design      462—464
Complex reassembly, docking and ligand design, free energies of binding      463—464
Complex reassembly, docking and ligand design, geometric issues      462—463
Complex reassembly, docking and ligand design, ranker energy ordering      463
Complex reassembly, docking and ligand design, success/failure ratios      463
Computational techniques, drug bioinformatics, target triage      484—486

1 2 3 4 5 6 7 8

О проекте