Clote P., Backofen R. — Computational Molecular Biology :: Электронная библиотека попечительского совета мехмата МГУ

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Clote P., Backofen R. — Computational Molecular Biology

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Название: Computational Molecular Biology

Авторы: Clote P., Backofen R.

Аннотация:

Primarily aimed at advanced undergraduate and graduate students from bioinformatics, computer science, statistics, mathematics and the biological sciences, this text will also interest researchers from these fields.

Язык:

Рубрика: Биология/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2000

Количество страниц: 287

Добавлена в каталог: 29.11.2005

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

Предметный указатель

Parallel $\beta$ sheets      16
Parallel mutations      137 138
Partition function      43 48 65
PDB format      266
Peptide bond      14
Percent minimization      59
Performance, definition      234—236
Periodicity rules      122
Persistence, definition      39
Phosphodiester bond      8
Phylogenetic trees      136 145 148
Pivot moves      232
Poisson distribution      29—30 34
Poisson process      138
Polar requirement      17
Polarity index      58
Polymer, definition      4
Polysaccharides      4
Positive transition matrix      42
Potential energy function      48
Primary structure      17 202
Principle of insufficient reason      63
Probability density function      25
Probability distributions      27—38
Probability function      24
Probability theory      23—53
Probability theory, exercises      72—73
Prokaryotes      1 19 20
Protein      2
Protein Data Bank (PDB)      266
Protein folding problem      201 see also folding
Protein motifs      194—195
Protein structure      15—17
Protein structure, prediction      201—262
Protein threading      202 246—259
Protein threading, definition      246—249
Proteins      14—19
Protokarya      2
Pulley Principle      162
Purines      8
Pyramidines      8
Quarternary structure      17
Quartet puzzling step      166—170
Quartet trees      166—168
Ramachandran plot      15
Random boolean cellular automation      74
Random sequence      118
Random variables      25—26 31
Re-estimation of parameters      180
Reciprocal translocation      119
Record-to-record Travel algorithm (RRT)      55
Recursion equation      92 95 104—107
Reference amino acid distance frequency      224
Relative threading      253
Restriction enzymes      81—82
Reverse transcriptases      83—84
Reversible Markov process      158
Ribose      7
Ribosomal RNA (rRNA)      13 21
Ribosomes      21
RNA      2 13
RNA polymerase      19 195
RNA secondary structure      202—213
Root mean square deviation (RMSD)      156
Roulette wheel technique      61
Saccharomyces cerevisiae      266
Saddlepoint      52
Salt bridges      17
SCOP database      266
Scoring a model      177—180
Scoring function      249 259
Scoring matrices      84—86
Scoring subsequence      113
Secondary structure      17 202
Secondary structure, elements      16
Segment algorithm      71
Segmentation algorithm      32
Selenocysteine      56
Sequence alignment      81—134
Sequence alignment, example      83—84
Sequence alignment, exercises      128—132
Sequence space      205
Shannon entropy function      64

Shannon's formula      62
Shape space      205
Shuffle algorithm      61
Shuffled-codon codes      56 58
Similarity methods      110—111
Simulated annealing      43—44 46 220
Simulated annealing, heuristics related to      54—55
Sinclair theorem      43
Single-molecule DNA sequencing      117
Small molecules      4—6
Small nuclear (snRNA)      13
Smith — Waterman local sequence alignment      120
Spacing constraints      248
Specific amino acid distance frequencies      225
Standard deviation      26
Standard error      31
Statistical model      175
statistical significance      69
StatSignificance algorithm      71
Steiner sequences      117—118
Stirling's approximation      146
Stirling's formula      24—25 62
Stochastic matrix      38
Strimmer, von Haeseler algorithm      168
Structure prediction      201—262
Structure prediction, constraint-based      243—246
Structure prediction, exercises      259—262
Sugar molecule      4
Sugar transport proteins      195
Sugars      6
Sum-of-pairs multiple sequence alignment problem      114
Supercoiled DNA      218 220
Supersecondary structures      16
Swiss-Prot      266
Synonymous substitutions      139
Syntenic distance      319 120
Synteny      119
Tandem duplication      99—110
TATA box      12 19 195—196
Taxon      137
Taylor expansion      29 143
Tertiary structure      17 201 202
Thermal luminescence      135
Threading sets      253
Threshold accepting (TA) algorithm      54—55
Thymine      8
Topological neighbors      229
Total free energy      220
Total probability formula      25
Trace matrix      93 98
Traceback      93 94 98 107 179 180
Transcription      19—21
Transfer RNA (tRNA)      13 20—21
Transition probability functions      141
Transitional mutations      140
transitions      110 127—128
Translation      19—21
Transposition      119
Transversion      110
Transversional mutations      140
TREE      145
Tree, likelihood      159—160
Tree, topology      166
Trypanosoma brucei      1
Trypanosomes      123—128
Ultrametric trees      147—52
Unger — Moult hybrid genetic algorithm      233
Unit evolutionary time      138
units of measurement      263—264
UPGMA      148—149 152 154—155 157
Uracil      8
Variance      26
Viterbi algorithm      180
Viterbi score of a model      179
WAC matrix      139
Water molecule      4
Waterman, Smith and Beyer theorem      95—96
Watson — Crick base pairs      121 124 205 209
Watson — Crick model      8
Watson — Crick rules      8
Web sites      266
WPGMA      151 156
Wraparound Dynamic Programming      107 108
Wraparound step      101 102

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