Structural Bioinformatics (Methods of Biochemical Analysis) 0471202002, 9780471202004
From the Foreword? "[A] must read for all of us committed to understanding the interplay of structure and function.
102 79 18MB
English Pages 681 [702] Year 2003
Table of contents :
COVER
TITLE
COPYRIGHT
CONTENTS
FOREWORD
PREFACE
ACKNOWLEDGMENTS
CONTRIBUTORS
Section I. INTRODUCTION
1. DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS
2. FUNDAMENTALS OF PROTEIN STRUCTURE
3. FUNDAMENTALS OF DNA AND RNA STRUCTURE
4. COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION
5. MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY
6. ELECTRON MICROSCOPY
7. MOLECULAR VISUALIZATION
Section II. DATA REPRESENTATION AND DATABASES
8. THE PDB FORMAT, mmCIF, AND OTHER DATA FORMATS
9. THE PROTEIN DATA BANK
10. THE NUCLEIC ACID DATABASE
11. OTHER STRUCTURE-BASED DATABASES
Section III. COMPARATIVE FEATURES
12. PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE
13. THE CATH DOMAIN STRUCTURE DATABASE
14. STRUCTURAL QUALITY ASSURANCE
15. ALL-ATOM CONTACTS: A NEW APPROACH TO STRUCTURE VALIDATION
16. STRUCTURE COMPARISON AND ALIGNMENT
Section IV. STRUCTURE AND FUNCTIONAL ASSIGNMENT
17. SECONDARY STRUCTURE ASSIGNMENT
18. IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS
19. INFERRING PROTEIN FUNCTION FROM STRUCTURE
Section V. PROTEIN INTERACTIONS
20. PREDICTION OF PROTEIN–PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION
21. ELECTROSTATIC INTERACTIONS
Section VI. PROTEINS AS DRUG TARGETS
22. PRINCIPLES AND METHODS OF DOCKING AND LIGAND DESIGN
23. STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY
Section VII. STRUCTURE PREDICTION
24. CASP AND CAFASP EXPERIMENTS AND THEIR FINDINGS
25. HOMOLOGY MODELING
26. FOLD RECOGNITION METHODS
27. AB INITIO METHODS
28. PREDICTION IN 1D: SECONDARY STRUCTURE, MEMBRANE HELICES, AND ACCESSIBILITY
Section VIII. THE FUTURE
29. STRUCTURAL GENOMICS
COLOR PLATES
INDEX
COVER
TITLE
COPYRIGHT
CONTENTS
FOREWORD
PREFACE
ACKNOWLEDGMENTS
CONTRIBUTORS
Section I. INTRODUCTION
1. DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS
2. FUNDAMENTALS OF PROTEIN STRUCTURE
3. FUNDAMENTALS OF DNA AND RNA STRUCTURE
4. COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION
5. MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY
6. ELECTRON MICROSCOPY
7. MOLECULAR VISUALIZATION
Section II. DATA REPRESENTATION AND DATABASES
8. THE PDB FORMAT, mmCIF, AND OTHER DATA FORMATS
9. THE PROTEIN DATA BANK
10. THE NUCLEIC ACID DATABASE
11. OTHER STRUCTURE-BASED DATABASES
Section III. COMPARATIVE FEATURES
12. PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE
13. THE CATH DOMAIN STRUCTURE DATABASE
14. STRUCTURAL QUALITY ASSURANCE
15. ALL-ATOM CONTACTS: A NEW APPROACH TO STRUCTURE VALIDATION
16. STRUCTURE COMPARISON AND ALIGNMENT
Section IV. STRUCTURE AND FUNCTIONAL ASSIGNMENT
17. SECONDARY STRUCTURE ASSIGNMENT
18. IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS
19. INFERRING PROTEIN FUNCTION FROM STRUCTURE
Section V. PROTEIN INTERACTIONS
20. PREDICTION OF PROTEIN–PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION
21. ELECTROSTATIC INTERACTIONS
Section VI. PROTEINS AS DRUG TARGETS
22. PRINCIPLES AND METHODS OF DOCKING AND LIGAND DESIGN
23. STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY
Section VII. STRUCTURE PREDICTION
24. CASP AND CAFASP EXPERIMENTS AND THEIR FINDINGS
25. HOMOLOGY MODELING
26. FOLD RECOGNITION METHODS
27. AB INITIO METHODS
28. PREDICTION IN 1D: SECONDARY STRUCTURE, MEMBRANE HELICES, AND ACCESSIBILITY
Section VIII. THE FUTURE
29. STRUCTURAL GENOMICS
COLOR PLATES
INDEX
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- Philip E. Bourne (editor)
- Helge Weissig (editor)
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