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.

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Рубрика: Физика/

Статус предметного указателя: Готов указатель с номерами страниц

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Год издания: 1998

Количество страниц: 435

Добавлена в каталог: 30.10.2005

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Предметный указатель

Synthesis sites, melting curves      225
Synthesis sites, probe distributions      222
Tan, Robert K. — Z.      369
Tandem mismatches, free energy parameters      248
Target binding, length dependence      217
Target duplex, Cartesian RMSD of refined structures      171
Target molecules, bridge between two probes      223
Target molecules, structures      114
Target oligonucleotides, sequences      221
TATA box, protein partner selection      329—345
TATA box-binding protein binding sites      330
TATA box-binding protein, DNA helix      329—345
TATA box-binding protein, RNA polymerase      329
Tautomeric form, nucleotide bases      1—2
TBP-bound DNA, local conformational properties and analysis      339—341
TBP-bound DNA, transient properties      341—342
Tectonics, RNA      346—358
Tetraloops, enhanced stability      249
Tetraloops, GnRA family      126
Tetraloops, RNA      293—295
Tetraloops, stability bonuses      251
Thermally bound state, macromolecular MD simulation      261
Thermodynamic parameters RNA folding      248
Thermodynamic parameters RNA secondary structure prediction      246—257
Thermodynamic properties, $\alpha$ -containing DNA duplexes      94
Thermodynamic stability RNA helices      352
Thermodynamic stability sequence dependent      255
Thermodynamic studies, RNA folding and DNA metabolism      9—10
Thermodynamic(s), duplex formation and mismatch discrimination      206—228
Thiviyanthan, Varatharasa      167
Thomas Jefferson University      92
Three-dimensional structure, large RNA molecules      6
Three-way junctions, single-stranded region      354
Thymidine glycol, stereoisomers      315
Thymine base damage, distortions of oligonucleotide      318
Thymine carbonyl vibrations in D      20
Thymine glycol in DNA, cis isomers      317
Thymine lesions, ring-saturated      313—318
Thymine, configuration      315
Thymine-derivative stereoisomers, relative stability      314
Tobacco mosaic virus, pseudoknotted three-way junction      351
Torsion angles, nucleic acid backbones      51—52
Torsion angles, parameters      107
Torsion angles, semiquantitative distance restraints      124
Torsion angles, variation      116
Torsional energy profile, nonbonded parameters      44 45
TpA steps, flexibility in response to changes      319 324
Transcription rate, accurate formation of functional RNA structures      231
Transformation(s), nab      384
Transformational set, homogeneous transformation matrices      396
Transition mechanism, B-DNA to A-DNA      297—299
Transition mutations, guanine reaction with alkylnitrosoureas      86
Translation, antibiotic bound to decoding site      376
Triangle smoothing, distance geometry      386
Triloops, enhanced stability      249
Triloops, stability bonuses      251
tRNA, adapter molecules      5
tRNA, clover-leaf model      5 6
tRNA, ribbon diagram      353
Trulson, Mark O.      206
Truncated probes, broadening and depression of melting curves      224
Truncated relaxation effects, correction      135
Turner, Douglas H.      246
Two-spin approximation, structural refinement      167—168
Two-spin approximation, systematic errors      168
Ultraviolet radiation, photocrosslink      374
Ulyanov, Nikolai B.      181
Uncertainty principle, terminology and notation      398—399
United atom representation, macromolecular systems      370

Universidad Autonoma de Barcelona      329
Universite de Montreal      394
Universite Pierre et Marie Curie      150
University of Alabama at Birmingham      369
University of Calgary      92 195
University of California at Berkeley      56
University of California at San Francisco      122 181 285
University of Dundee      77
University of Illinois at Chicago, The      18
University of Maryland at Baltimore      304
University of Minnesota      41
University of Oregon      150
University of Rochester      246
University of San Francisco      285
University of Southampton      77
University of Texas Health Science Center      405
University of Texas Medical Branch      167
University of Vermont      360
University of Warsaw      285
Uracil, lowest energy k and lone-pair ionization potentials      22
UV-induced mutations, dipyrimidine sequences      313
Valence electronic structure, nucleotides      18
van Batenburg, F. H. D.      229
van de Sande, Johan H.      92
van der Waals parameters      43—44
VanLoock, Margaret S.      369
Variable-length linkers, coaxial stacking of helices      363
Viroid RNA, conserved metastable hairpin      244
Viroid RNA, metastable hairpins for efficient replication      231
Viroid(s), photoreactive motif within internal loop B      361
Vogel, Hans J.      195
Walter, N.      360
Walton, Ian D.      206
Washington University      246
Water activity, DNA conformational transitions      278
Water activity, stabilization of A — DNA      296—297
Water docking, dimethyl phosphate and dimethyl phosphorothioate models      44
Water structure, base pairs in internal loops      71
Water-counterion environments, energetics of nucleotide ionization      18—40
Watson-Crick base pairs, $G\cdot C$ and $A\cdot T$       78
Watson-Crick base pairs, complementarity      77—79
Watson-Crick base pairs, duplex structures      77
Watson-Crick base pairs, hydrogen bond stabilization      79
Watson-Crick base pairs, identification      129
Watson-Crick base pairs, isosteric in antiparallel helices      347
Watson-Crick base pairs, sequence and conformational junctions      161
Watson-Crick hydrogen bonds base pairs near cis-syn thymine dimer      323
Wayne State University      1
Weinstein, Harel      329
Wesleyan University      260
Westhof, Eric      346
Wobble configuration, purine-pyrimidine, pair      80
Wobble pair, NH protons      129
Wormlike chain model, DNA      12
X-PLOR, molecular modeling problem      380
X-PLOR, pseudoknot      386
X-PLOR, starting model coordinates      174
X-ray crystal structures, RNA internal loops      56—76
X-ray fiber diffraction analysis, RNA samples      6
X-ray fiber diffraction data, B-form DNA      2
yammp, molecular modeling problem      380
Yeast $tRNA^{asp}$ , ribbon diagram      353
Yeast $tRNA^{Phe}$ , $Pb^{2+}$ cleavage of specific ribophosphodiester bond      402
Young, M. A.      260
Z DNA, alternating cytosine and guanine      159
Zhou, Ning      195
Zhu, Frank      167
Zuker, Michael      246
Zwieb, Christian      405
Zwitterion radicals, base ionization      37

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