Polarity index in proteins : a bioinformatics tool / by Carlos Polanco. -- Sharjah : Bentham Science Publishers, 2016. – (58.17115/P762)

Contents

FOREWORD

PREFACE

ACKNOWLEDGEMENTS  iv

ACRONYMS

PART 1   PART I-PRELIMINARIES

CHAPTER 1  MACROMOLECULES  3

      1.1. THE LIVING AND NON-LIVING ENTITIES  3

      1.2. PROTEINS  5

      1.3. THE WATER  12

      1.4. CONSIDERATIONS  13

      REFERENCES  13

CHAPTER 2  ELECTROMAGNETIC STABILITY  15

      2.1. IONIZATION ENERGY  15

      2.2. CHEMICAL BONDS  15

      2.3. CONSIDERATIONS  20

      REFERENCES  21

PART 2  PART II-FOUNDATIONS

CHAPTER 3  POLARITY INDEX METHOD  22

      3.1. SUPERVISED ALGORITHMS  22

      3.2. QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP MODELS  22

      3.3. POLARITY INDEX METHOD  24

      3.4. CONSIDERATIONS  26

      REFERENCES  27

CHAPTER 4  MATHEMATICAL FOUNDATION

      4.1. SMOOTH CURVES

      4.2. SINGULARITIES AND REGULARITIES  30

      4.3. CATASTROPHIC BIFURCATION POINTS  30

      4.4. MATRIX

      4.5. CONSIDERATIONS

      REFERENCES

CHAPTER 5  COMPUTATIONAL IMPLEMENTATION

      5.1. TYPES OF PROCESSING  33

      5.2. MICROPROCESSING

      5.3. AIMS & FOCUS

      5.4. CONSIDERATIONS

      REFERENCES

CHAPTER 6  PATHOGENIC BACTERIA

     6.1. FUNCTIONALITY

      6.2. CURRENT TAXONOMY  37

      6.3. BACTERIA

      6.4. VIRUSES

      6.5. FUNGI

      6.6. CANCER CELLS    45

      6.7. SIMILARITIES AND DIFFERENCES  47

      6.8. SPECIAL NOTES

      6.9. CONSIDERATIONS

      REFERENCES

PART 3  PART III-STRUCTURAL PROPERTIES

CHAPTER 7  CELL PENETRATING PEPTIDES

      7.1. DESCRIPTION

      7.2. SIMILARITIES AND DIFFERENCES  55

      7.3. SPECIAL NOTES  y.  56

      7.4. CONSIDERATIONS  56

      REFERENCES  56

CHAPTER 8  AMYLOID PROTEINS  59

      8.1. PROTEIN FOLDING  59

      8.2. POLAR PROFILE  59

      8.3. LIPOPROTEINS  60

      8.4. NATIVELY UNFOLDED PROTEINS  61

      8.5. PARTIALLY FOLDED PROTEINS  63

      8.6. NATIVELY FOLDED PROTEINS  64

      8.7. NEURONS PROTEINS   65

      8.8. SIMILARITIES AND DIFFERENCES  66

      8.9. SPECIAL NOTES  68

      8.10. CONSIDERATIONS  68

      REFERENCES  69

CHAPTER 9  GLOBULAR & FIBROUS PROTEINS  71

      9.1. PRELIMINARIES  71

      9.2. GLOBULAR PROTEINS  71

      9.3. FIBROUS PROTEINS  72

      9.4. SIMILARITIES AND DIFFERENCES  74

      9.5. SPECIAL NOTES  75

      9.6. CONSIDERATIONS  75

      REFERENCES  75

PART 2  PART IV-BIOGENESIS & TRENDS

CHAPTER 10  BIOGENETIC EXPERIMENTS  77

      10.1. BIOGENESIS  77

      10.2. MILLER & UREY: PRIMORDIAL SOUP  78

      10.3. FOX & HARADA: PROTEINOIDS  79

      10.4. RODE: DIPEPTIDES  81

      10.5. SIMILARITIES AND DIFFERENCES  84

      10.6. CONSIDERATIONS  86

      REFERENCES  87

CHAPTER 11  FUTURE DIRECTIONS  89

      11.1. PROTEOMICS TRENDS  89

      11.2. DISTRIBUTED COMPUTING  90

      11.3. SYNTHETIC PROTEINS

      11.4. BIOINFORMATICS

      11.5. CONSIDERATIONS

      REFERENCES

APPENDIX A-COMPUTATIONAL TOOLS  93

      A.1. PRELIMINARIES

      A.2. PREPARATION FILES

      A.3. POLARITY INDEX METHOD PROGRAM  96

      A.4. OUTPUT DATASETS

APPENDIX B-PROTEIN DATABASES

      B.1. APD2 DATABASE

      B.2. AMYPDB DATABASE

      B.3. UNIPROT DATABASE

      B.4. CPPSITE DATABASE

      B.5. SCAAP DATASET

      B.6. AMYLOIDOSIS DATASETS

      B.7. CONSIDERATIONS

      REFERENCES

GLOSSARY

      REFERENCES

SUBJECT INDEX