| Preface |
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ix | |
| Introduction |
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xi | |
| Author |
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xvii | |
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Chapter One Protein Structure Fundamentals and Complexity |
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1 | (32) |
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1 | (7) |
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B Levels of Protein Structure |
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8 | (6) |
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C Why Are Proteins So Complicated? Chemical Considerations |
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14 | (7) |
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D Why Are Proteins So Complicated? Structural Considerations |
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21 | (4) |
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E Why Are Proteins So Complicated? Biological Considerations |
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25 | (2) |
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27 | (3) |
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Notes, Sources, and Further Reading |
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30 | (3) |
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Chapter Two Essentials of Information |
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33 | (24) |
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33 | (2) |
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B Queries, Information, and Probability |
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35 | (9) |
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C Probability Sets and Information Vectors |
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44 | (5) |
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D Information and Protein Sequences |
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49 | (4) |
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53 | (2) |
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Notes, Sources, and Further Reading |
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55 | (2) |
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Chapter Three Protein Structure Analysis at the Base Level |
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57 | (44) |
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57 | (14) |
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B A Digression on Sets and Partitions |
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71 | (3) |
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C Partition Applications and Experiments |
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74 | (5) |
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D Base Structures and Variations |
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79 | (10) |
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E Sequences, Variations, and Structure Reciprocity |
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89 | (6) |
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95 | (3) |
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Notes, Sources, and Further Reading |
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98 | (3) |
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Chapter Four Base Structure Analysis and Constituent Numbers |
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101 | (26) |
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A Sequences, Bases, and Compressibility |
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101 | (5) |
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B Natural Sets and W-Distributions |
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106 | (12) |
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C Sequence N and Information Asymmetry |
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118 | (4) |
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122 | (3) |
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Notes, Sources, and Further Reading |
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125 | (2) |
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Chapter Five Base Structures and Proteomic Sets |
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127 | (30) |
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A Sequences, Base Structures, and Sets |
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127 | (8) |
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B Set Structures, Partitions, and Information Economy |
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135 | (5) |
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C Set Structures and Shape Properties |
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140 | (6) |
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D Sets and Internal Structures |
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146 | (7) |
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153 | (1) |
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Notes, Sources, and Further Reading |
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153 | (4) |
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Chapter Six Protein Structure Analysis of Base-plus Levels |
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157 | (30) |
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157 | (7) |
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B Base+ Structures and Information Gaps |
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164 | (5) |
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C Base+ Structures and Information Scaling Properties |
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169 | (3) |
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D Interval Structures and Information Scaling |
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172 | (5) |
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E Base+ Structures and Numerical Information Scaling |
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177 | (3) |
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F Base+ Structures and Natural Sets |
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180 | (3) |
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183 | (1) |
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Notes, Sources, and Further Reading |
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184 | (3) |
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Chapter Seven Analysis of Sequences Internal to Proteins |
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187 | (32) |
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187 | (5) |
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B Covalent Paths, Information, and Sets |
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192 | (5) |
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C Paths, Information Vectors, and Pair Distributions |
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197 | (13) |
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D Paths, Information Vectors, and Deviations |
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210 | (4) |
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214 | (2) |
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Notes, Sources, and Further Reading |
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216 | (3) |
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Chapter Eight Writing and Refining Protein Sequences |
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219 | (36) |
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219 | (4) |
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B Altering Motifs to Obtain New Sequences |
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223 | (15) |
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C Expanding Templates to Obtain New Sequences |
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238 | (6) |
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D Writing Sequences from Scratch |
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244 | (8) |
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252 | (1) |
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Notes, Sources, and Further Reading |
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253 | (2) |
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255 | (10) |
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264 | (1) |
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Sources and Further Reading |
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264 | (1) |
| Appendix One Select Properties of the Amino Acids |
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265 | (6) |
| Appendix Two Essential Properties of Steady-State Systems |
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271 | (2) |
| Appendix Three The Stirling Formula for Large Factorials |
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273 | (4) |
| Appendix Four The Binomial and Multinomial Distributions |
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277 | (2) |
| Appendix Five Amino Acids and the Genetic Code |
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279 | (2) |
| Appendix Six Accession Details for Relevant Sequences and Sets |
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281 | (4) |
| Appendix Seven Answers to Selected Exercises |
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285 | (4) |
| Index |
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289 | |