Structural Bioinformatics, 2nd Edition

CONTENTS

Foreword

Preface

Acknowledgments

Contributors

Section I DATA COLLECTION, ANALYSIS, AND VISUALIZATION

1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS

WHAT IS BIOINFORMATICS?

TECHNICAL CHALLENGES WITHIN STRUCTURAL BIOINFORMATICS

INTEGRATING STRUCTURAL DATA WITH OTHER DATA SOURCES

REFERENCES

2 FUNDAMENTALS OF PROTEIN STRUCTURE

THE IMPORTANCE OF PROTEIN STRUCTURE

THE PRIMARY STRUCTURE OF PROTEINS: THE AMINO ACID SEQUENCE

THE SECONDARY STRUCTURE OF PROTEINS: THE LOCAL THREE-DIMENSIONAL STRUCTURE

THE TERTIARY STRUCTURE OF PROTEINS: THE GLOBAL THREE-DIMENSIONAL STRUCTURE

THE QUATERNARY STRUCTURE OF PROTEINS: ASSOCIATIONS OF MULTIPLE POLYPEPTIDE CHAINS

CONCLUSION

MORE INFORMATION ON THE INTERNET

REFERENCES

3 FUNDAMENTALS OF DNA AND RNA STRUCTURE

INTRODUCTION

CHEMICAL STRUCTURE OF NUCLEIC ACIDS

BASE-PAIR GEOMETRY

CONFORMATION OF THE SUGAR PHOSPHATE BACKBONE

STRUCTURES OF NUCLEIC ACIDS

CONCLUSION

ACKNOWLEDGMENTS

REFERENCES

4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION

INTRODUCTION

HIGH-THROUGHPUT STRUCTURE DETERMINATION

DATA ANALYSIS

HEAVY ATOM LOCATION AND COMPUTATION OF EXPERIMENTAL PHASES

DENSITY MODIFICATION

MOLECULAR REPLACEMENT

REFINEMENT

VALIDATION

CHALLENGES TO AUTOMATION

CONCLUSIONS

REFERENCES

5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY

INTRODUCTION TO PROTEIN STRUCTURE DETERMINATION BY NMR

PREPARATION OF PROTEIN SAMPLES FOR NMR

PROTOCOL FOR PROTEIN STRUCTURE DETERMINATION BY NMR

PROBA BILISTIC ...