Leontis N.B. (ed.), SantaLucia J., Jr. (ed.) — Molecular Modeling Of Nucleic Acids :: Электронная библиотека попечительского совета мехмата МГУ

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Leontis N.B. (ed.), SantaLucia J., Jr. (ed.) — Molecular Modeling Of Nucleic Acids

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Название: Molecular Modeling Of Nucleic Acids

Авторы: Leontis N.B. (ed.), SantaLucia J., Jr. (ed.)

Аннотация:

Covering numerous topics in modeling nucleic acids, this volume looks at the role of various spectroscopic methods, simulations of molecular dynamics using particle mesh methods, and dynamic and genetic algorithms for predicting RNA secondary structure. It also covers the thermodynamics of nucleic acid folding and three-dimensional structure prediction based on sequence information.

Язык:

Рубрика: Физика/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 1998

Количество страниц: 435

Добавлена в каталог: 30.10.2005

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Предметный указатель

$Na^{+}$ counterions, influence on gas-phase ionization potentials      30—34
$RNA\cdot\alpha$ -winged ODN hybrids, denaturing gel electrophoretic analysis of RNase H digestion products      95f
$\alpha$ -anomeric nucleotides, base stacking and specific base pairing      103
$\alpha$ -containing decamer duplexes, ${}^{31}$ P NMR spectra      104
$\alpha$ -containing decamer duplexes, imino proton region      98 3
$\alpha$ -containing decamer duplexes, sequences      96
$\alpha$ -containing decamer duplexes, sugar puckering data      100
$\alpha$ -containing decamer duplexes, thermodynamic data      971
$\alpha$ -containing DNA duplexes, spectroscopic studies      94 103
$\alpha$ -winged ODN, RNA targets      94
$\alpha$ -winged ODN/RNA duplexes, cleavage by RNase H      92 94
$\alpha$ -winged RNase H substrates, sequences and control      95
$\alpha$ A decamer duplexes, models      102
$\alpha$ C decamer, pathways      99
$\alpha$ T decamer, studies      103
$\beta-\alpha-\beta$ stretch, schematic diagram      93
$^{1}H NMR$ spectra of $\alpha T2$ imino proton and methyl group regions      104
$^{31}P NMR$ , backbone conformation of duplexes      100
3-Hydroxytetrahydrofuran, photoelectron spectra, molecular orbital diagrams, and IPs      20f
3D NOE-NOE refinements, quality      173
3D NOESY-NOESY refinement, methods      174—176
3D NOESY-NOESY refinement, simulation study      170
9-Methyladenine, photoelectron spectra, molecular orbital diagrams, and IPs      21f
A-DNA, stabilized by hydration and counterion association in major groove      299
A-DNA, structure stabilization      297
A-form geometry, stability      296
A-tract DNA, interpretation of Raman bands      152 155
A-tract DNA, measurement and assignments of Raman bands      151 152
A-tract DNA, solution structure away from crystal packing constraints      164
A-tract-T-tract (bent) DNA, molecular modeling      155 159
ab initio methods, quantum mechanical, calculations      7 8
Acid-base titration, native DNA      2
Adenine H2 protons, partial relaxation correction      137
Adenosine platforms, same strand pairing      74
Adsorption density, probe sites      213
Adsorption density, saturating match and mismatch      226
Adsorption equilibrium, probe sites      213 217
Adsorption isotherms, matched probes      214
Adsorption kinetics, change with time for matched probes      212
Adsorption kinetics, duplex formation      211 213
Adsorption to probes, matched and single-base mismatched      214
Affymetrix      206
Algorithms, genetic      229 245
AMBER, all-hydrogen parameter sets      304
AMBER, counterion equilibration      174
AMBER, distrance constraints      175
AMBER, electrostatic potential energy      319
AMBER, energy functions      262
AMBER, energy minimization      113
AMBER, nab molecular mechanics package      386
AMBER, refinement calculations      140
AMBER, sodiums within contact distance with phosphates      333
AMBER, spontaneous transitions between A and B forms of DNA      305
AMBER3.0, force field results      266 270
AMBER4.0, ring-saturated thymine derivatives      318
AMBER4.1, conformational behavior of oligonucleotides in aqueous solution      289
AMBER4.1, DNA conformational transitions      278
AMBER4.1, dynamical models of oligonucleotide sequences      274
AMBER4.1, model compound calculations      45
AMBER4.1, model compounds for parameterization      44
AMBER4.1, molecular simulations      48—49
AMBER4.1, simulating proteins and nucleic acids      43
AMBER4.1, simulation of mlp      331
Amino acid, sequence SPXX in nuclear proteins      195 204
Andre, Troy C.      246
Anisotropic duplexes, cross-relaxation rate, constants      111
Anisotropic motions, nucleic acids      110 111
Antiparallel P-sheet motif, binds to minor, groove      196
Antisense DNA therapy, gene expression      92
Antisense drugs, phosphorothioates      42 43
Antisense drugs, properties      92
Antisense oligonucleotides, design and characterization      41 42
Antisense oligonucleotides, nuclease-resistant a-anomeric segments      103
ApT pocket, minor groove      270
ApT pocket, structural detail of $Na^{+}$ ion      272
Aqueous bulk solvation, nucleotide Gibbs, free energies of activation      34 37
Aramini, James M.      92
Artificial nuclease, activity      163
Assembly rules, RNA mosaic units      350 355
Atom truncation, MD simulations of nucleic, acids      304
Atomic resolution models, ribosomal decoding site      372 374
Atomic-level models, nucleic acid, structures      379
Axis bending, DNA sequences      270
Axis bending, spontaneous      274
B — RNA, simulation      288
B-DNA, crystal structures      263—265
B-DNA, marker band      154
B-form trajectory, hydroxyl groups      51
B-form trajectory, protrusion of      2
B-form trajectory, sugar puckering      53
B/Z junctions, double      162
B/Z junctions, location in T-tract-CG-tract-A-tract deoxy oligonucleotides      159—163
B/Z junctions, nuclease attack      151
Backbone conformation, influence on A to B equilibrium      307 310
Backbone torsion angles, molecular dynamics      140
Backbone torsion angles, restraints      124
Backbone torsion angles, variable in polynucleotides      4
Backbone, changes in nucleotide conformations      118
Backbone, degrees of freedom      115
Backbone-sugar torsions, helicoidal, parameters      381
Backfolding, nuclease hypersensitive sites      412
Banerjee, A. R.      360
Base inclination energy, A and B forms of DNA      309
Base locations, construction      381
Base orbitals, comparisons      28
Base orbitals, molecular orbital diagrams      29
Base pair step parameters      3411 3421
Base pair step(s), conformation      337 338
Base pair(s), constraining a nucleotide      253
Base pair(s), duplex oligonucleotides, hydrogen bonding patterns      77—90
Base pair(s), isolated      253
Base pair(s), percent correctly predicted      254
Base pair(s), phylogenetically determined      246
Base pair(s), scoring against phylogenetic structures      253
Base pair(s), terminal fraying      291
Base pairing, algorithms and computer programs      3
Base pairing, DNA and RNA      2
Base pairing, severe weakening      319
Base sequence, local DNA structure      2—3
Base stacking, ab initio study      8
Base stacking, RNA      352
Base-first strategies, nucleic acid modeling      381
Belief and plausibility measures, structural hypothesis      402
Bendability, DNA      330 343
Bending angles, repair of photodamaged DNA      293
Bending Dials, bending in structures      261
Bending, DNA bound by TBP      339
Berzal — Herranz, A.      360
Beveridge, D. L.      260
Bifurcated hydrogen bonds, Raman measurements of carbonyl vibrations      159
Billed, Todd M.      122
Binding affinity, chirality of phos-phorothioate center      43
Binding sites, ribozyme      72
Biograf, DNA models      150
Biograf, energy minimization      155—159
Biological evolution, RNA molecules      347
Biological RNA molecules, internal loops      57
Biomolecule, nuclear spins      10
Biphasic kinetics, cleavage and ligation kinetics      364
Biphasic kinetics, ribozyme      360
BMS, parameter set      304
Bond, J.      360
Bounds object, distance geometry      385
Bowling Green State University      1 167
Bridged structures, length dependence      217
Bridging interactions, target concentrations      226
Brown, Tom      77
Bulk hydration, energetic ordering of ionization events      35—37
Bulk hydration, ionization energies of nucleotide clusters      35
Burke, J. M.      360

Butcher, S.      360
C++ folding algorithm      248
C++ RNA secondary structure prediction      246
Carbonyl environment, bent and straight DNA      159
Carcinogenicity, structure of photodamaged DNA oligomers      291
Case, David A.      379
Catalytic activity, folded structure of RNA      361
Cellulaire du Centre National de la Recherche Scientifique      346
Chain growth, rate of energy improvement      237—238
Chain length, A-tract — T-tract DNA      156
CHARMM      23
CHARMM, all-hydrogen parameter sets      304
CHARMM, consecutive phosphorus-phosphorus distances      334 335
CHARMM, energy functions      262
CHARMM, force fields with balanced solute-solvent and solvent-solvent interactions      286
CHARMM, periodic boundary conditions for hexagonal prism      331
CHARMM, spontaneous transitions between A and B forms of DNA      305
CHARMM, structure on sodium-sodium rdf      333
CHARMM, transitions observed in DNA helices      294
Cheatham, T. E., Ill      285
Chemical changes to DNA, test case for modeling      289—291
Chemical crosslinking, tRNA-mRNA complex      373
Chemical damage, modified base      86
Chemical shift, changes in peptide-DNA hairpin samples      202 203
Chemical shift, database      118
Chemical shift, peptide — DNA sample      199
Chirality, A- and B-form geometries      41—54
Cieplak, P.      285
Cleavage activity, prevention      363
Cleavage kinetics, chase step      364
Cleavage reactions, single-turnover conditions      367
Cleavage, fluorescence energy transfer signal      364
Clover-leaf model, tRNA      5 6
Clusters, $5’ -dTMP^{-} and 5’ -dCMP^{-}$       32
Clusters, optimization calculations      31
Clusters, structures of      5
Coaxial stacking, helixes      250 363
Coaxial stacking, three-way junction      366
Coaxial stacking, two helixes with intervening mismatch      252
Coaxially oriented helices, SRP RNA      407 410
Code statistics, nab      383
Codon-anticodon interactions, degeneracy of genetic code      80
Cognate DNA sequence, propensity to distort      278
CombiChem, Inc      285
Comparative modeling of      3
Comparative sequence analysis, deducing secondary structures from primary sequence      5—6
Comparative sequence analysis, SRP RNA secondary structures      406
Compensatory base changes, mutations      406
Competing equilibria, probes and target binding      223—224
Computer calculations, quantum mechanical      8
Computer experiment, MD simulation      260—263
Computer folded sequences, approximating free energy parameters of structural motifs      247
Computer language, MC-SYM      380
Computer language, nab      379—393
Computer language, OCL      381
Computer language, X-PLOR      380
Computer language, yammp      380
Computer modeling, characteristics      394—395
Computer modeling, genetic algorithm      229—245
Computer modeling, three-dimensional RNA structures      394—404
Computer software, AMBER      113 140—146 174 175 262 304—311 386
Computer software, AMBER3.0      266—270
Computer software, AMBER4.1      43 45 48 9 274 278 289 331
Computer software, Bending Dials      261
Computer software, BIOGRAF      150 155—159
Computer software, BMS      304
Computer software, C      246 248
Computer software, CHARMM      262 304—311
Computer software, CHARMM23      286 294 331
Computer software, CORMA      184 185—186 189
Computer software, CURVES      68 261 318 331
Computer software, D      405—413
Computer software, Dials and Windows      261 307 318 331
Computer software, DNAminiCarlo      184 185 186 189
Computer software, efn      2 250—252
Computer software, ERNA      3
Computer software, FELIX      174
Computer software, GAUSSIAN      90 314
Computer software, GROMOS      262 265—266
Computer software, Insight II      113 331
Computer software, JUMNA      381
Computer software, MARDIGRAS      124—146 184—186 189
Computer software, MC-SYM      373 395
Computer software, MEDUSA      182 189
Computer software, Metropolis Monte Carlo      184
Computer software, Mfold      246 248
Computer software, mlp      331
Computer software, Molecular Dynamics Tool Chest      261
Computer software, MORASS      174
Computer software, MORCAD      381
Computer software, NEW HELIX      93 156 159
Computer software, Newhelix      261
Computer software, OPLS      286
Computer software, PARSE      182—183 189
Computer software, PDQPRO      185 186 193
Computer software, QUANTA      331
Computer software, RANDMARDI      184
Computer software, SHAKE      290 331
Computer software, Simulaid      331
Computer software, X-PLOR      174 386
Configuration, mRNA-tRNA complexes      372—373
Conformation build-up procedures, nucleic acid modeling      380—381
Conformation, nucleic acids in solution      118
Conformational change, RNA tetraloop      294
Conformational degrees of freedom, duplex DNA      312
Conformational dynamics, DNA backbone torsions      261
Conformational dynamics, spontaneous A-DNA to B-DNA transitions      287
Conformational flexibility, biological, functioning      11
Conformational hell, escape      361—363
Conformational junctions, nonstraight DNA      159—163
Conformational pool, potential conformers for DNA dinucleotide      186
Conformational preferences, calculated and X-ray crystallographic data      315
Conformational preferences, ring-saturated thymine derivatives      313 318
Conformational sampling, problem in simulations      298
Conformational sampling, results of conformer ensemble refinement      189—193
Conformational sampling, structural ensembles      181—194
Conformational sampling, structure of nucleic acids in solution      299—300
Conformational search space, molecular contacts      396—397
Conformational space, base pair step parameters for DNA oligomers      341
Conformational space, RNA      395
Conformational transition, barriers      288
Conformers, generation and selection      183
Conformers, potential      182—183 (see also Potential conformers)
Constraints, factors affecting number and accuracy      108—118
Constraints, structure determination      108
Controlled flexibility, nucleic acids      380
Cooney, Michael      312
CORMA, dipole-dipole relaxation rates      186
CORMA, NOE intensities for each ensemble      185 186 189
CORMA, relaxation rates and NOE intensities      184
CORMA, relaxation rates for potential conformers      185
Cornell et al. force field, conformational behavior of oligo-nucleotides in aqueous solution      289
Cornell et al. force field, DNA conformational transitions      278
Cornell et al. force field, generality      291
Cornell et al. force field, MD simulations on nucleic acid systems      285—303
Correlation function, nucleic acids      111
COSY crosspeaks, estimates of coupling constants      108
Counterion association, A-DNA, stabilization      299
Counterion condensation, MD results and theory predictions      270
Counterion density, MD calculated around duplex      271
Coupling constants, averaging      111
Coupling constants, deoxy sugar      117
Coupling constants, mole fractions and phase angles      112
Coupling constants, torsion angles      108—109
Cross-relaxation rate constants, intemuclear separation and correlation time      110
Cross-relaxation rate constants, spin diffusion      109
Crossover operations, parental solutions      237
Crosspeaks, DQF — COSY spectrum      126
Crosspeaks, intensity difference      137
Crystal conformation, pseudorotational, angle plots      157

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