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Invitation to Protein Sequence Analysis Through Probability and Information [Kõva köide]

  • Formaat: Hardback, 292 pages, kõrgus x laius: 254x178 mm, kaal: 720 g, 271 Illustrations, black and white
  • Ilmumisaeg: 04-Feb-2019
  • Kirjastus: CRC Press
  • ISBN-10: 0367134527
  • ISBN-13: 9780367134525
  • Formaat: Hardback, 292 pages, kõrgus x laius: 254x178 mm, kaal: 720 g, 271 Illustrations, black and white
  • Ilmumisaeg: 04-Feb-2019
  • Kirjastus: CRC Press
  • ISBN-10: 0367134527
  • ISBN-13: 9780367134525

This book explores the remarkable information correspondences and probability structures of proteins. Correspondences are pervasive in biochemistry and bioinformatics: proteins share homologies, folding patterns, and mechanisms. Probability structures are just as paramount: folded state graphics reflect Angstrom-scale maps of electron density. The author explores protein sequences (primary structures), both individually and in sets (systems) with the help of probability and information tools. This perspective will enhance the reader’s knowledge of how an important class of molecules is designed and put to task in natural systems, and how we can approach class members in hands-on ways.

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